diff --git a/.gitignore b/.gitignore
index 6db21e1..6682ca9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,6 @@
+# Hail run logs
+hail-*.log
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
diff --git a/1-import_data/1-import_gatk_vcfs_to_hail.py b/1-import_data/1-import_gatk_vcfs_to_hail.py
index cd13efc..5ba152e 100644
--- a/1-import_data/1-import_gatk_vcfs_to_hail.py
+++ b/1-import_data/1-import_gatk_vcfs_to_hail.py
@@ -1,42 +1,63 @@
 # Load GATK VCFs into hail and save as matrixtable
-import hail as hl
 import pyspark
 import yaml
 import os
 import sys
-from wes_qc.utils.utils import parse_config
+import re
+import hail as hl
+from utils.utils import parse_config, path_local, path_spark
 
+# DEBUG: for some reason, paths prefix is `file:`, not a `file://`
+VCF_PATTERN = re.compile("file:.*vcf.b?gz")
 
-def load_vcfs_to_mt(indir, outdir, tmp_dir, header):
+def load_vcfs_to_mt(config):
     '''
-    load VCFs and save as hail mt
+    load VCFs and save as hail mt.  
+    Save mt as outdir/gatk_unprocessed.mt
+
+    ### Config fields
+    ```
+    step1.gatk_vcf_header_infile
+    step1.gatk_vcf_indir
+    step1.gatk_mt_outfile
+    ```
     '''
-    objects = hl.utils.hadoop_ls(indir)
-    vcfs = [vcf["path"] for vcf in objects if (vcf["path"].startswith("file") and vcf["path"].endswith("vcf.gz"))]
-    print("Loading VCFs")
+    indir, header, outfile = (
+        config['step1']['gatk_vcf_indir'], 
+        config['step1'].get('gatk_vcf_header_infile'), # optional
+        config['step1']['gatk_mt_outfile']
+    )
+
+    objects = hl.utils.hadoop_ls(path_spark(indir))
+    
+    # get paths of all vcf files
+    vcfs = [vcf["path"] for vcf in objects if VCF_PATTERN.match(vcf["path"])]
+    print(f"info: Found {len(vcfs)} VCFs in {indir}")
     #create and save MT
-    mt = hl.import_vcf(vcfs, array_elements_required=False, force_bgz=True, header_file = header)
-    print("Saving as hail mt")
-    mt_out_file = outdir + "gatk_unprocessed.mt"
+    if header:
+        print("info: Loading VCFs with header")
+        mt = hl.import_vcf(vcfs, array_elements_required=False, force_bgz=True, header_file=header)
+    else:
+        print("info: Loading VCFs WITHOUT header")
+        mt = hl.import_vcf(vcfs, array_elements_required=False, force_bgz=True)
+        
+    mt_out_file = path_spark(outfile)
+    print(f"Saving as hail mt to {mt_out_file}")
     mt.write(mt_out_file, overwrite=True)
 
-
 def main():
     #set up input variables
-    inputs = parse_config()
-    vcf_header = inputs['gatk_vcf_header']
-    import_vcf_dir = inputs['gatk_import_lustre_dir']
-    mtdir = inputs['matrixtables_lustre_dir']
-
+    config = parse_config()
+    
     #initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
-    hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    tmp_dir = config['general']['tmp_dir']
+    # sc = pyspark.SparkContext()
+    sc = pyspark.SparkContext.getOrCreate()
+    hadoop_config = sc._jsc.hadoopConfiguration() # unused
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
     #load VCFs
-    load_vcfs_to_mt(import_vcf_dir, mtdir, tmp_dir, vcf_header)
-
+    load_vcfs_to_mt(config)
 
 if __name__ == '__main__':
-    main() 
\ No newline at end of file
+    main() 
diff --git a/2-sample_qc/1-hard_filters_sex_annotation.py b/2-sample_qc/1-hard_filters_sex_annotation.py
index 5b775e2..f9cdd0b 100644
--- a/2-sample_qc/1-hard_filters_sex_annotation.py
+++ b/2-sample_qc/1-hard_filters_sex_annotation.py
@@ -1,68 +1,104 @@
 #apply gnomad's hard filters and impute sex
 #input gatk_unprocessed.mt from step 1.1
+import os
 import hail as hl
+import hailtop.fs as hfs
 import pyspark
-from utils.utils import parse_config
+from utils.utils import parse_config, path_local, path_spark
+import os
 
-def apply_hard_filters(mt: hl.MatrixTable, mtdir: str) -> hl.MatrixTable:
+def apply_hard_filters(mt: hl.MatrixTable, config: dict) -> hl.MatrixTable:
     '''
     Applies hard filters and annotates samples in the filtered set with call rate
     :param MatrixTable mt: MT containing samples to be ascertained for sex
     :param str mtdir: directory output matrix tables are written to
+    :param dict config:
     :return: MatrixTable with hard filtering annotation
     :rtype: MatrixTable
+
+    ### Config fields
+    step2.sex_annotation_hard_filters.filtered_mt_outfile : path  
+    step2.sex_annotation_hard_filters.n_alt_alleles_threshold : float  
+    step2.sex_annotation_hard_filters.defined_gt_frac_threshold : float  
     '''
+    conf = config['step2']['sex_annotation_hard_filters']
+
     print("Applying hard filters")
-    filtered_mt_file = mtdir + "mt_hard_filters_annotated.mt"
+    filtered_mt_file = path_spark(conf['filtered_mt_outfile']) # output
+
     mt = mt.filter_rows((hl.len(mt.alleles) == 2) & hl.is_snp(mt.alleles[0], mt.alleles[1]) &
-        (hl.agg.mean(mt.GT.n_alt_alleles()) / 2 > 0.001) &
-        (hl.agg.fraction(hl.is_defined(mt.GT)) > 0.99))
+        (hl.agg.mean(mt.GT.n_alt_alleles()) / 2 > conf['n_alt_alleles_threshold']) &
+        (hl.agg.fraction(hl.is_defined(mt.GT)) > conf['defined_gt_frac_threshold']))
     mt = mt.annotate_cols(callrate=hl.agg.fraction(hl.is_defined(mt.GT)))
     mt.write(filtered_mt_file, overwrite=True)
 
     return mt
 
 
-def impute_sex(mt: hl.MatrixTable, mtdir: str, annotdir: str, male_threshold: float = 0.8, female_threshold: float = 0.5) -> hl.MatrixTable:
+def impute_sex(mt: hl.MatrixTable, config: dict) -> hl.MatrixTable:
     '''
     Imputes sex, exports data, and annotates mt with this data
     :param MatrixTable mt: MT containing samples to be ascertained for sex
-    :param str mtdir: directory output matrix tables are written to
-    :param str annotdir: directory annotation files are written to
+    :param dict config:
     :return: MatrixTable with imputed sex annotations stashed in column annotation 'sex_check'
     :rtype: MatrixTable
+
+    ### Config fields
+    step2.impute_sex.sex_ht_outfile : path  
+    step2.impute_sex.sex_mt_outfile : path  
+    step2.impute_sex.female_threshold : float  
+    step2.impute_sex.male_threshold : float  
+    step2.impute_sex.aaf_threshold : float  
     '''
-    print("Imputing sex with male_threshold = " + str(male_threshold) + " and female threshold = " + str(female_threshold))
+
+    conf = config['step2']['impute_sex']
+    print("Imputing sex with male_threshold = " + str(conf['male_threshold']) + " and female threshold = " + str(conf['female_threshold']))
 
     #filter to X and select unphased diploid genotypes - no need to filter to X as impute_sex takes care of this
     #mt1 = hl.filter_intervals(mt, [hl.parse_locus_interval('chrX')])
     mt1 = hl.split_multi_hts(mt)
     mtx_unphased = mt1.select_entries(GT=hl.unphased_diploid_gt_index_call(mt1.GT.n_alt_alleles()))
     #imput sex on the unphased diploid GTs
-    sex_ht = hl.impute_sex(mtx_unphased.GT, aaf_threshold=0.05, female_threshold=female_threshold, male_threshold=male_threshold)
+    sex_ht = hl.impute_sex(mtx_unphased.GT, aaf_threshold=conf['aaf_threshold'], female_threshold=conf['female_threshold'], male_threshold=conf['male_threshold'])
     #export
-    sex_ht.export(annotdir + '/sex_annotated.sex_check.txt.bgz')
+    sex_ht.export(path_spark(conf['sex_ht_outfile'])) # output
     #annotate input (all chroms) mt with imputed sex and write to file
     sex_colnames = ['f_stat', 'is_female']
     sex_ht = sex_ht.select(*sex_colnames)
     mt = mt.annotate_cols(**sex_ht[mt.col_key])
-    sex_mt_file = mtdir + "mt_sex_annotated.mt"
+    sex_mt_file = path_spark(conf['sex_mt_outfile']) # output
     print("Writing to " + sex_mt_file)
     mt.write(sex_mt_file, overwrite=True)
 
     return mt
 
 
-def identify_inconsistencies(mt: hl.MatrixTable, mtdir: str, annotdir: str, resourcedir: str):
+def identify_inconsistencies(mt: hl.MatrixTable, config: dict):
     '''
     Find samples where annotated sex conflicts with the sex in our metadata
     Find samples where sex is not annotated
-    Find samples where f_stat is between 0.2 and 0.8
+    Find samples where f_stat is between fstat_low and fstat_high
     :param MatrixTable mt: MT containing imputed sex in column 'sex_check'
-    :param str mtdir: directory output matrix tables are written to
-    :param str annotdir: directory annotation files are written to
-    :param str resourcedir: directory annotation files are written to
+    :param dict config:
+
+    ### Config fields
+    step2.sex_inconsistencies.sex_metadata_file : input path : TODO explain metadata structure and constants  
+    step2.sex_inconsistencies.conflicting_sex_report_file : output path : TODO  
+    step2.sex_inconsistencies.fstat_outliers_report_file : output path : TODO  
+    step2.sex_inconsistencies.fstat_low : float  
+    step2.sex_inconsistencies.fstat_high : float  
     '''
+    conf = config['step2']['sex_inconsistencies']
+
+    # TODO: do we need such a detailed logging, or a single if (... and ... and ...) will suffice?
+    error = False
+    if not hfs.exists(conf['sex_metadata_file']):
+        print("error: identify_inconsistencies: missing input: sex_metadata_file")
+        error = True
+    if error:
+        print("skip identify_inconsistencies because of previous errors")
+        return
+
     print("Annotating samples with inconsistencies:")
     qc_ht = mt.cols()
     #convert is_female boolean to sex
@@ -73,8 +109,8 @@ def identify_inconsistencies(mt: hl.MatrixTable, mtdir: str, annotdir: str, reso
     qc_ht = qc_ht.annotate(sex=sex_expr).key_by('s')
 
     #annotate with manifest sex - keyed on ega to match identifiers in matrixtable
-    metadata_file =  resourcedir +  '/mlwh_sample_and_sex.txt'
-    metadata_ht = hl.import_table(metadata_file, delimiter="\t").key_by('accession_number')
+
+    metadata_ht = hl.import_table(path_spark(conf['sex_metadata_file']), delimiter="\t").key_by('accession_number')
     #we only want those from the metadata file where sex is known
     metadata_ht = metadata_ht.filter((metadata_ht.gender == 'Male') | (metadata_ht.gender == 'Female'))
 
@@ -84,41 +120,45 @@ def identify_inconsistencies(mt: hl.MatrixTable, mtdir: str, annotdir: str, reso
     #identify samples where imputed sex and manifest sex conflict
     conflicting_sex_ht = ht_joined.filter(((ht_joined.sex == 'male') & (ht_joined.manifest_sex == 'Female')) | (
         (ht_joined.sex == 'female') & (ht_joined.manifest_sex == 'Male')))
-    conflicting_sex_ht.export(annotdir + '/conflicting_sex.txt.bgz')
 
-    #identify samples where f stat is between 0.2 and 0.8
-    f_stat_ht = qc_ht.filter( (qc_ht.f_stat > 0.2) & (qc_ht.f_stat < 0.8) )
-    f_stat_ht.export(annotdir + '/sex_annotation_f_stat_outliers.txt.bgz')
+    # TODO: do we need this redundancy? the paths already have the "file://" prefix
+    conflicting_sex_ht.export(path_spark(conf['conflicting_sex_report_file'])) # output
+
+    #identify samples where f stat is between fstat_low and fstat_high
+    f_stat_ht = qc_ht.filter( (qc_ht.f_stat > conf['fstat_low']) & (qc_ht.f_stat < conf['fstat_high']) )
+    f_stat_ht.export(path_spark(conf['fstat_outliers_report_file'])) # output
     
 
 def main():
     #set up
-    inputs = parse_config()
+    config = parse_config()
     #importmtdir = inputs['load_matrixtables_lustre_dir']
-    mtdir = inputs['matrixtables_lustre_dir']
-    annotdir = inputs['annotation_lustre_dir']
-    resourcedir = inputs['resource_dir']
 
-    #initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    #initialise hailS
+    tmp_dir = config['general']['tmp_dir']
+    # sc = pyspark.SparkContext()
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
-    mt_in_file = mtdir + "/gatk_unprocessed.mt"
+    mt_infile = config['step1']['gatk_mt_outfile'] # input from 1.1
     print("Reading input matrix")
-    mt_unfiiltered = hl.read_matrix_table(mt_in_file)
+    mt_unfiltered = hl.read_matrix_table(path_spark(mt_infile))
 
     #apply hard fitlers
-    mt_filtered = apply_hard_filters(mt_unfiiltered, mtdir)
+    mt_filtered = apply_hard_filters(mt_unfiltered, config)
 
     #impute sex
-    mt_sex = impute_sex(mt_filtered, mtdir, annotdir, male_threshold=0.6)
+    mt_sex = impute_sex(mt_filtered, config)
 
+    # TODO: where is this function?
     # annotate_ambiguous_sex(mt_sex, mtdir)
-    identify_inconsistencies(mt_sex, mtdir, annotdir, resourcedir)
-
 
+    # TODO: make this optional and check how it affects the downstream steps
+    # there is no metadata for our contrived test datasets
+    #identify_inconsistencies
+    identify_inconsistencies(mt_sex, config)
+    
 if __name__ == '__main__':
     main() 
 
diff --git a/2-sample_qc/2-prune_related_samples.py b/2-sample_qc/2-prune_related_samples.py
index 0c5b2f4..781968f 100644
--- a/2-sample_qc/2-prune_related_samples.py
+++ b/2-sample_qc/2-prune_related_samples.py
@@ -1,122 +1,200 @@
 # identify and prune related samples prior to PCA
 # use mt with hard filters and sex annotation from 2-sample_qc/1-hard_filters_sex_annotation.py
 import hail as hl
+import os
 import pyspark
-from wes_qc.utils.utils import parse_config
-from bokeh.plotting import save, output_file
+from utils.utils import parse_config, subdict, multigetp, path_local, path_spark
+import bokeh.plotting as bkplt
 
 
-def prune_mt(mtin: hl.MatrixTable, mtoutfile: str):
+def prune_mt(mtin: hl.MatrixTable, config: dict) -> hl.MatrixTable:
     '''
     Splits multiallelic sites and runs ld pruning
     Filter to autosomes before LD pruning to decrease sample size - autosomes only wanted for later steps
     :param MatrixTable mtin: input MT containing variants to be pruned
-    :param str mtdir: directory output matrix tables are written to
+    :param dict config:
+    :return: Pruned MatrixTable
+    :rtype: hl.MatrixTable
+
+    `hl.ld_prune` returns a maximal subset of variants that are nearly uncorrelated within each window.
+    Requires the dataset to contain only diploid genotype calls and no multiallelic variants.
+    See also: https://hail.is/docs/0.2/methods/genetics.html#hail.methods.ld_prune
+
+    ### Config fields
+    step2.prune.pruned_mt_file : output path  
+    step2.prune.r2 : float  
+
+    ### Optional ld_prune arguments  
+    step2.prune.ld_prune_args.bp_window_size : int optional  
+    step2.prune.ld_prune_args.memory_per_core : int optional  
+    step2.prune.ld_prune_args.keep_higher_maf : bool optional  
+    step2.prune.ld_prune_args.block_size : int optional  
     '''
+    conf = config['step2']['prune']
+    ld_prune_args = conf['ld_prune_args']
+    mtoutfile = conf['pruned_mt_file']
+
     print("Filtering to autosomes")
     mtin = mtin.filter_rows(mtin.locus.in_autosome())
     print("Splitting multiallelic sites")
     # mtin = hl.split_multi(mtin)
     mtin = hl.split_multi_hts(mtin)#this shouldn't do anything as only biallelic sites are used
     print("Performing LD pruning")
-    pruned_ht = hl.ld_prune(mtin.GT, r2=0.2)
+    pruned_ht = hl.ld_prune(mtin.GT, **ld_prune_args)
     pruned_mt = mtin.filter_rows(hl.is_defined(pruned_ht[mtin.row_key]))
     pruned_mt = pruned_mt.select_entries(GT=hl.unphased_diploid_gt_index_call(pruned_mt.GT.n_alt_alleles()))
-    pruned_mt.write(mtoutfile, overwrite=True)
+    pruned_mt.write(path_spark(mtoutfile), overwrite=True) # output
+
+    return pruned_mt
 
 
-def run_pc_relate(pruned_mt_file: str, relatedness_ht_file: str, samples_to_remove_file: str, scores_file: str):
+def run_pc_relate(pruned_mt: hl.MatrixTable, config: dict) -> hl.MatrixTable:
     '''
     Runs PC relate on pruned MT
-    :param str pruned_mt_file: ld pruned MT file
-    :param str relatedness_ht_file: relatedness ht file
-    :param str samples_to_remove_file: file samples to remove ht is written to
-    :param str scores_file: file scores ht is written to
+    :param hl.MatrixTable pruned_mt: ld pruned MT file
+    :param dict config:
+    :return: mt with a column of too related samples to remove
+    :rtype: hl.MatrixTable
+
+    See https://hail.is/docs/0.2/methods/relatedness.html#hail.methods.pc_relate
+
+    ### Config fields
+    step2.pc_relate.relatedness_ht_file : output path : relatedness ht file  
+    step2.pc_relate.samples_to_remove_file : output path : ht file with a list of samples to remove  
+    step2.pc_relate.scores_file : output path: : ht file with hwe_normalized_pca scores  
+    step2.pc_relate.pca_components : int : number of components for the hwe_normalized_pca   
+    step2.pc_relate.relatedness_column : str : pc_relate output column to use when applying the relatedness_threshold  
+    step2.pc_relate.relatedness_threshold : float : samples with relatedness_column greater than relatedness_threshold are to be removed  
+
+    ### Optional config fields
+    step2.pc_relate.pc_relate_args.min_individual_maf : float  
+    step2.pc_relate.pc_relate_args.block_size : float  
+    step2.pc_relate.pc_relate_args.min_kinship : float  
+    step2.pc_relate.pc_relate_args.statistics : str  
+    step2.pc_relate.pc_relate_args.k : int  
+    step2.pc_relate.pc_relate_args.include_self_kinship : bool  
     '''
+    conf = config['step2']['prune_pc_relate']
+    pc_relate_kwargs = conf['pc_relate_args']
+
     print("Running PC relate")
-    pruned_mt = hl.read_matrix_table(pruned_mt_file)
-    eig, scores, _ = hl.hwe_normalized_pca(pruned_mt.GT, k=10, compute_loadings=False)
-    scores.write(scores_file, overwrite=True)
+
+    # TODO: DEBUG: k=10 didn't work for the small test dataset, throwing an error:
+    # "Error summary: IllegalArgumentException: requirement failed: Dimension mismatch!: _a.cols == _b.rows (11 != 10)"
+    eig, scores, _ = hl.hwe_normalized_pca(pruned_mt.GT, k=conf['pca_components'], compute_loadings=False)
+    scores.write(path_spark(conf['scores_file']), overwrite=True) # output
 
     print("Calculating relatedness")
-    relatedness_ht = hl.pc_relate(pruned_mt.GT, min_individual_maf=0.05, scores_expr=scores[pruned_mt.col_key].scores, block_size=4096, min_kinship=0.05, statistics='kin2')
-    relatedness_ht.write(relatedness_ht_file, overwrite=True)
-    #prune individuals to be left with unrelated - creates a table containing one column - samples to remove
-    pairs = relatedness_ht.filter(relatedness_ht['kin'] > 0.125)
+    relatedness_ht = hl.pc_relate(pruned_mt.GT, scores_expr=scores[pruned_mt.col_key].scores, **pc_relate_kwargs)
+    relatedness_ht.write(path_spark(conf['relatedness_ht_file']), overwrite=True) # output
+    
+    # prune individuals to be left with unrelated - creates a table containing one column - samples to remove
+    rel_col = conf['relatedness_column']
+    rel_threshold = conf['relatedness_threshold']
+
+    pairs = relatedness_ht.filter(relatedness_ht[rel_col] > rel_threshold)
     related_samples_to_remove = hl.maximal_independent_set(pairs.i, pairs.j, keep=False)
-    related_samples_to_remove.write(samples_to_remove_file, overwrite=True)   
+    related_samples_to_remove.write(path_spark(conf['samples_to_remove_file']), overwrite=True) # output
+
+    return related_samples_to_remove
 
 
-def run_population_pca(pruned_mt_file: str, pca_mt_file: str, mtdir: str, plotdir: str, samples_to_remove_file: str):
+# How is this step different from 2-sample_qc/3-population_pca_prediction.py / run_pca ?
+# Only PCA plotting?
+def run_population_pca(pruned_mt: hl.MatrixTable, samples_to_remove: hl.Table, config: dict) -> hl.MatrixTable:
     '''
     Runs PCA and creates a matrix table of non-related individuals with PCA scores
     Remove related samples from PC relate from pruned MT and run PCA
-    :param str pruned_mt_file: ld pruned MT file
-    :param str pca_mt_file: PCA output MT file
-    :param str mtdir: directory output matrix tables are written to
-    :param str plotdir: directory output plots are written to
-    :param str samples_to_remove_file: related samples to remove ht file
+    :param hl.MatrixTable pruned_mt: ld pruned MT
+    :param hl.Table samples_to_remove_file: a HT with a single column of related samples to remove 
+    :param dict config:
+    :param str pca_mt_file: PCA output MT file path TODO move to config
+    :return: TODO
+    :rtype: hl.MatrixTable
+
+    ### Config fields
+    step2.population_pca.plink_outfile : output path : TODO  
+    step2.population_pca.pca_components : int : TODO  
+    step2.population_pca.pca_scores_file : output path : TODO  
+    step2.population_pca.pca_loadings_file : output path : TODO  
+    step2.population_pca.pca_mt_file : output path : TODO  
+    step2.population_pca.plot_outfile : output path : Bokeh PCA scatterplot  
+
     '''
+    conf = config['step2']['prune_plot_pca']
+    plinkfile = conf['plink_outfile']
+    pca_scores_file = conf['pca_scores_file']
+    pca_loadings_file = conf['pca_loadings_file']
+    pca_mt_file = conf['pca_mt_file']
+
     print("Running population PCA")
-    pruned_mt = hl.read_matrix_table(pruned_mt_file)
     print("Removing related samples")
-    related_samples_to_remove = hl.read_table(samples_to_remove_file)
-    pca_mt = pruned_mt.filter_cols(hl.is_defined(related_samples_to_remove[pruned_mt.col_key]), keep=False)
+    pca_mt = pruned_mt.filter_cols(hl.is_defined(samples_to_remove[pruned_mt.col_key]), keep=False)
     variants, samples = pca_mt.count()
     print(f"{samples} samples after relatedness step.")
 
     plink_mt = pca_mt.annotate_cols(uid=pca_mt.s).key_cols_by('uid')
-    plinkfile = mtdir + "mt_unrelated.plink"
-    hl.export_plink(plink_mt, plinkfile,fam_id=plink_mt.uid, ind_id=plink_mt.uid)
+    hl.export_plink(dataset=plink_mt, output=path_spark(plinkfile), fam_id=plink_mt.uid, ind_id=plink_mt.uid) # output
 
     print("Running PCA")
-    pca_evals, pca_scores, pca_loadings = hl.hwe_normalized_pca(pca_mt.GT, k=20, compute_loadings=True)
+
+    # TODO: DEBUG: k=20 didn't work for the small test dataset
+    # Error summary: IllegalArgumentException: requirement failed: Requested k singular values but got k=20 and numCols=9.
+    pca_evals, pca_scores, pca_loadings = hl.hwe_normalized_pca(pca_mt.GT, k=conf['pca_components'], compute_loadings=True)
     pca_af_ht = pca_mt.annotate_rows(pca_af=hl.agg.mean(pca_mt.GT.n_alt_alleles()) / 2).rows()
     pca_loadings = pca_loadings.annotate(pca_af=pca_af_ht[pca_loadings.key].pca_af)
-    pca_scores_file = mtdir + "mt_pca_scores.ht"#table of pca scores per sample
-    pca_scores.write(pca_scores_file, overwrite=True)
-    pca_loadings_file = mtdir + "mt_pca_loadings.ht"#table of SNPs, PCA loadings and AF
-    pca_loadings.write(pca_loadings_file, overwrite=True)
+    pca_scores.write(path_spark(pca_scores_file), overwrite=True) # output
+    pca_loadings.write(path_spark(pca_loadings_file), overwrite=True) # output
     pca_mt = pca_mt.annotate_cols(scores=pca_scores[pca_mt.col_key].scores)
-    pca_mt.write(pca_mt_file, overwrite=True)
+    pca_mt.write(path_spark(pca_mt_file), overwrite=True) # output
 
     print("Plotting PC1 vs PC2")
+    plot_outfile = path_local(conf['plot_outfile'])
+    os.makedirs(os.path.dirname(plot_outfile), exist_ok=True)
+
     p = hl.plot.scatter(pca_mt.scores[0], pca_mt.scores[1], title='PCA', xlabel='PC1', ylabel='PC2')
-    output_file(plotdir + "pca.html")
-    save(p)
+    print(f'saving plot to {plot_outfile} DEBUG') # DEBUG
+    bkplt.output_file(plot_outfile)
+    bkplt.save(p)
+
+    return pca_mt
 
 
 
 def main():
     #set up
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
-    plotdir = inputs['plots_lustre_dir']
+    config = parse_config()
 
-    #initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    #initialise hailS
+    tmp_dir = config['general']['tmp_dir']
+    # sc = pyspark.SparkContext()
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
+
+    #ensure plotting directory exists
+    pltdir = path_local(config['general']['plots_dir'])
+    if not os.path.exists(pltdir):
+        os.makedirs(pltdir)
 
     #load input mt
-    mtfile = mtdir + "mt_sex_annotated.mt"
-    mt = hl.read_matrix_table(mtfile)
+    # mt_infile = os.path.join(mtdir, "mt_sex_annotated.mt")
+    mt_infile = config['step2']['impute_sex']['sex_mt_outfile']
+    mt = hl.read_matrix_table(path_spark(mt_infile))
 
     #ld prune to get a table of variants which are not correlated
-    pruned_mt_file = mtdir + "mt_ldpruned.mt"
-    prune_mt(mt, pruned_mt_file)
+    # pruned_mt_file = os.path.join(mtdir, "mt_ldpruned.mt")
+    pruned_mt = prune_mt(mt, config)
 
     #run pcrelate
-    relatedness_ht_file = mtdir + "mt_relatedness.ht"
-    samples_to_remove_file = mtdir + "mt_related_samples_to_remove.ht"
-    scores_file = mtdir + "mt_pruned.pca_scores.ht"
-    run_pc_relate(pruned_mt_file, relatedness_ht_file, samples_to_remove_file, scores_file)
+    # relatedness_ht_file = os.path.join(mtdir, "mt_relatedness.ht")
+    # samples_to_remove_file = os.path.join(mtdir, "mt_related_samples_to_remove.ht")
+    # scores_file = os.path.join(mtdir, "mt_pruned.pca_scores.ht")
+    related_samples_to_remove_ht = run_pc_relate(pruned_mt, config)
 
     #run PCA
-    pca_mt_file = mtdir + "mt_pca.mt"
-    run_population_pca(pruned_mt_file, pca_mt_file, mtdir, plotdir, samples_to_remove_file)
+    population_pca_mt = run_population_pca(pruned_mt, related_samples_to_remove_ht, config)
 
 
 if __name__ == '__main__':
-    main() 
\ No newline at end of file
+    main() 
diff --git a/2-sample_qc/3-population_pca_prediction.py b/2-sample_qc/3-population_pca_prediction.py
index 69734f2..f7320d0 100644
--- a/2-sample_qc/3-population_pca_prediction.py
+++ b/2-sample_qc/3-population_pca_prediction.py
@@ -1,10 +1,13 @@
 # population prediction with PCA
 import hail as hl
 import pyspark
+import os
 import argparse
 import pandas as pd
+from typing import Optional
 from gnomad.sample_qc.ancestry import assign_population_pcs
-from wes_qc.utils.utils import parse_config
+from utils.utils import parse_config
+from utils.config import path_local, path_spark
 
 def get_options():
     '''
@@ -23,50 +26,62 @@ def get_options():
         help="assign populations", action="store_true")
     parser.add_argument("-r", "--run",
         help="run all steps except kg_to_mt", action="store_true")
+
     args = parser.parse_args()
 
     return args
     
 
-def create_1kg_mt(resourcedir: str, mtdir: str):
+def create_1kg_mt(config: dict):
     '''
     Create matrixtable of 1kg data
     :param str resourcedir: resources directory
     :param str mtdir: matrixtable directory
     '''
-    indir = resourcedir + "1kg_vcfs_filtered_by_wes_baits/"
-    vcfheader = indir + "header.txt"
+    conf = config['step2']['create_1kg_mt']
+
+    # TODO: correct resource dir: /lustre/scratch126/WES_QC/resources/1000g_VCFs
+    indir = path_spark(conf['indir'])
+    vcfheader = conf['vcfheader'] # TODO: DEBUG: not used during tests on small dataset
     objects = hl.utils.hadoop_ls(indir)
     vcfs = [vcf["path"] for vcf in objects if (vcf["path"].startswith("file") and vcf["path"].endswith("vcf.gz"))]
     print("Loading VCFs")
     #create and save MT
-    mt = hl.import_vcf(vcfs, array_elements_required=False, force_bgz=True, header_file = vcfheader)
+    # TODO: make header optional (don't have one for mini 1000g test)
+    mt = hl.import_vcf(vcfs, array_elements_required=False, force_bgz=True)
     print("Saving as hail mt")
-    mt_out_file = mtdir + "kg_wes_regions.mt"
+    mt_out_file = path_spark(conf['mt_out_file'])
     mt.write(mt_out_file, overwrite=True)
 
+    return mt
+
 
-def merge_with_1kg(pruned_mt_file: str, mtdir: str, merged_mt_file: str):
+def merge_with_1kg(pruned_mt_file: hl.MatrixTable, config: dict) -> hl.MatrixTable:
     '''
     merge the birth cohort WES ld-pruned data with 1kg data of known population
     :param str pruned_mt_file: ld pruned MT file
     :param str mtdir: resources directory
     :param str merged_mt_file: merged output MT file
     '''
+    conf = config['step2']['merge_with_1_kg']
     print("Merging with 1kg data")
-    mt = hl.read_matrix_table(pruned_mt_file)
-    kg_mt_file = mtdir + "kg_wes_regions.mt"
+    # mt = hl.read_matrix_table(pruned_mt_file)
+    mt = pruned_mt_file # FIXME: just testing accepting mt instead of a path
+    kg_mt_file = path_spark(conf['kg_mt_file'])
     kg_mt = hl.read_matrix_table(kg_mt_file)
     # in order to create a union dataset the entries and column fields must be 
     # the same in each dataset. The following 2 lines take care of this.
     kg_mt = kg_mt.select_entries(kg_mt.GT)
-    mt = mt.drop('callrate', 'f_stat', 'is_female')
+    mt = mt.drop('callrate', 'f_stat', 'is_female') # TODO: move to config or not? seems to be specific to the qc pipeline so no need to make variable
     # union cols gives all samples and the rows which are found in both
     mt_joined = mt.union_cols(kg_mt)
+    merged_mt_file = path_spark(conf['merged_mt_outfile'])
     mt_joined.write(merged_mt_file, overwrite=True)
 
+    return mt_joined
 
-def annotate_and_filter(merged_mt_file: str, resourcedir: str, filtered_mt_file: str):
+
+def annotate_and_filter(merged_mt_file: hl.MatrixTable, config: dict) -> hl.MatrixTable:
     '''
     Annotate with known pops for 1kg samples and filter to remove long range LD regions, 
     rare variants, palidromic variants, low call rate and HWE filtering
@@ -74,8 +89,10 @@ def annotate_and_filter(merged_mt_file: str, resourcedir: str, filtered_mt_file:
     :param str resourcedir: resources directory
     :param str filtered_mt_file: merged birth cohort wes and 1kg MT file annotated with pops and filtered
     '''
+    conf = config['step2']['annotate_and_filter']
     print("Adding population annotation for 1kg samples")
-    mt = hl.read_matrix_table(merged_mt_file)   
+    # mt = hl.read_matrix_table(merged_mt_file)
+    mt = merged_mt_file
 
     # The following annotates by population
     # pops_file = resourcedir + "integrated_call_samples.20130502.ALL.ped"
@@ -83,18 +100,21 @@ def annotate_and_filter(merged_mt_file: str, resourcedir: str, filtered_mt_file:
     # mt = mt.annotate_cols(known_pop=cohorts_pop[mt.s].Population)
 
     # The following is 1kg superpop
-    pops_file = resourcedir + "/igsr_samples.tsv"
+
+    # TODO: remove leading slash
+    pops_file = path_spark(conf['pops_file'])
     cohorts_pop = hl.import_table(pops_file, delimiter="\t").key_by('Sample name')
     mt = mt.annotate_cols(known_pop=cohorts_pop[mt.s]['Superpopulation code'])
 
     print("Filtering variants")
     mt_vqc = hl.variant_qc(mt, name='variant_QC_Hail')
     mt_vqc_filtered = mt_vqc.filter_rows(
-        (mt_vqc.variant_QC_Hail.call_rate >= 0.99) &
-        (mt_vqc.variant_QC_Hail.AF[1] >= 0.05) &
-        (mt_vqc.variant_QC_Hail.p_value_hwe >= 1e-5)
+        (mt_vqc.variant_QC_Hail.call_rate >= conf['call_rate']) &
+        (mt_vqc.variant_QC_Hail.AF[1] >= conf['AF']) &
+        (mt_vqc.variant_QC_Hail.p_value_hwe >= conf['p_value_hwe'])
     )
-    long_range_ld_file = resourcedir + "long_range_ld_regions_chr.txt"
+    # TODO: this file must be .bed (?)
+    long_range_ld_file = path_spark(conf['long_range_ld_file'])
     long_range_ld_to_exclude = hl.import_bed(long_range_ld_file, reference_genome='GRCh38')
     mt_vqc_filtered = mt_vqc_filtered.filter_rows(hl.is_defined(long_range_ld_to_exclude[mt_vqc_filtered.locus]), keep=False)
     mt_non_pal = mt_vqc_filtered.filter_rows((mt_vqc_filtered.alleles[0] == "G") & (mt_vqc_filtered.alleles[1] == "C"), keep=False)
@@ -102,10 +122,13 @@ def annotate_and_filter(merged_mt_file: str, resourcedir: str, filtered_mt_file:
     mt_non_pal = mt_non_pal.filter_rows((mt_non_pal.alleles[0] == "A") & (mt_non_pal.alleles[1] == "T"), keep=False)
     mt_non_pal = mt_non_pal.filter_rows((mt_non_pal.alleles[0] == "T") & (mt_non_pal.alleles[1] == "A"), keep=False)
 
+    filtered_mt_file = path_spark(conf['filtered_mt_outfile'])
     mt_non_pal.write(filtered_mt_file, overwrite=True)
 
+    return mt_non_pal
+
 
-def run_pca(filtered_mt_file: str, pca_scores_file: str, pca_loadings_file: str, pca_evals_file: str):
+def run_pca(filtered_mt_file: hl.MatrixTable, config: dict):
     '''
     Run PCA before population prediction
     :param str filtered_mt_file: merged birth cohort wes and 1kg MT file annotated with pops and filtered
@@ -113,18 +136,28 @@ def run_pca(filtered_mt_file: str, pca_scores_file: str, pca_loadings_file: str,
     :param str pca_loadings_file: PCA scores HT file
     :param str pca_evals_file: PCA scores HT file
     '''
-    mt = hl.read_matrix_table(filtered_mt_file)
+    conf = config['step2']['run_pca']
+    # mt = hl.read_matrix_table(filtered_mt_file)
+    mt = filtered_mt_file # FIXME: testing accepting mt
     #exclude EGAN00004311029 this is a huge outlier on PCA and skews all the PCs
-    to_exclude = ['EGAN00004311029']
+    to_exclude = ['EGAN00004311029'] # TODO: add as a list parameter to the config
     mt = mt.filter_cols(~hl.set(to_exclude).contains(mt.s)) 
-    pca_evals, pca_scores, pca_loadings = hl.hwe_normalized_pca(mt.GT, k=10, compute_loadings=True)
+
+    # TODO: move k to config
+    pca_evals, pca_scores, pca_loadings = hl.hwe_normalized_pca(mt.GT, k=4, compute_loadings=True)
     pca_scores = pca_scores.annotate(known_pop=mt.cols()[pca_scores.s].known_pop)
+    pca_scores_file = path_spark(conf['pca_scores_outfile'])
     pca_scores.write(pca_scores_file, overwrite=True)
+    pca_loadings_file = path_spark(conf['pca_loadings_outfile'])
     pca_loadings.write(pca_loadings_file, overwrite=True)
+    pca_evals_file = path_local(conf['pca_evals_outfile'])
+
     with open(pca_evals_file, 'w') as f:
         for val in pca_evals:
             f.write(str(val) + "\n")
 
+    # don't return anything as there are multiple outputs
+
 
 def append_row(df, row):
     return pd.concat([
@@ -133,16 +166,23 @@ def append_row(df, row):
            ).reset_index(drop=True)
 
 
-def predict_pops(pca_scores_file: str, pop_ht_file: str, pop_ht_tsv):
+def predict_pops(config: dict):
     '''
     Predict populations from PCA scores
     :param str pca_sores_file: PCA scores HT file
     :param str pop_ht_file: predicted population HT file
     :param str pop_ht_tsv: population tsv file
     '''
+    conf = config['step2']['predict_pops']
+    pca_scores_file = path_spark(conf['pca_scores_file'])
     pca_scores = hl.read_table(pca_scores_file)
     known_col = "known_pop"
-    pop_ht, pop_clf = assign_population_pcs(pca_scores, pca_scores.scores, known_col=known_col, n_estimators=100, prop_train=0.8, min_prob=0.5)
+    pop_ht, pop_clf = assign_population_pcs(pca_scores, pca_scores.scores, 
+                                            known_col=known_col, 
+                                            n_estimators=conf['gnomad_pc_n_estimators'], 
+                                            prop_train=conf['gnomad_prop_train'], 
+                                            min_prob=conf['gnomad_min_prob'])
+    pop_ht_file = path_spark(conf['pop_ht_outfile'])
     pop_ht.write(pop_ht_file, overwrite=True)
     #convert to pandas and put in only pops files, add excluded sample back
     pop_ht_df = pop_ht.to_pandas()
@@ -150,6 +190,8 @@ def predict_pops(pca_scores_file: str, pop_ht_file: str, pop_ht_tsv):
     new_row = pd.Series({'s':'EGAN00004311029', 'pop':'oth'})
     pop_ht_df2 = append_row(pop_ht_df2, new_row)
     print(pop_ht_df2)
+
+    pop_ht_tsv = path_local(conf['pop_ht_outtsv'])
     print(pop_ht_tsv)
 
     pop_ht_df2.to_csv(pop_ht_tsv, sep = '\t')
@@ -166,47 +208,49 @@ def predict_pops(pca_scores_file: str, pop_ht_file: str, pop_ht_tsv):
 
 
 def main():
-    #set up
+    # get cli args
     args = get_options()
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
-    resourcedir = inputs['resource_dir']
-    mtdir2 = inputs['load_matrixtables_lustre_dir']
+    config = parse_config()
+    tmp_dir = config['general']['tmp_dir']
+    mtdir = config['general']['matrixtables_dir']
 
     #initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    # tmp_dir = "hdfs://spark-master:9820/"
+    # sc = pyspark.SparkContext()
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
     #if needed, create 1kg matrixtable
     if args.kg_to_mt:
-        create_1kg_mt(resourcedir, mtdir)
+        # the output is not used in this main func
+        created_1kg_mt = create_1kg_mt(config)
 
     #combine with 1KG data
-    pruned_mt_file = mtdir + "mt_ldpruned.mt"
-    merged_mt_file = mtdir + "merged_with_1kg.mt"
     if args.merge or args.run:
-        merge_with_1kg(pruned_mt_file, mtdir, merged_mt_file)
+        pruned_mt_file = path_spark(os.path.join(mtdir, 'mt_ldpruned.mt'))
+        pruned_mt = hl.read_matrix_table(pruned_mt_file)
+
+        # the output is not used in this main func
+        mt_joined = merge_with_1kg(pruned_mt, config)
 
     #annotate and filter
-    filtered_mt_file = mtdir + "merged_with_1kg_filtered.mt"
     if args.filter or args.run:
-        annotate_and_filter(merged_mt_file, resourcedir, filtered_mt_file)
+        merged_mt_file = path_spark(config['step2']['merge_with_1_kg']['merged_mt_outfile'])
+        merged_mt = hl.read_matrix_table(merged_mt_file)
+        
+        # the output is not used in this main func
+        mt_non_pal = annotate_and_filter(merged_mt, config)
 
     #run pca
-    pca_scores_file = mtdir + "pca_scores_after_pruning.ht"
-    pca_loadings_file = mtdir + "pca_loadings_after_pruning.ht"
-    pca_evals_file = mtdir2 + "pca_evals_after_pruning.txt"#text file may need to be without file///
     if args.pca or args.run:
-        run_pca(filtered_mt_file, pca_scores_file, pca_loadings_file, pca_evals_file)
+        filtered_mt_file = path_spark(config['step2']['annotate_and_filter']['filtered_mt_outfile'])
+        filtered_mt = hl.read_matrix_table(filtered_mt_file)
+        run_pca(filtered_mt, config)
 
     #assign pops
-    pop_ht_file = mtdir + "pop_assignments.ht"
-    pop_ht_tsv = mtdir2 + "pop_assignemtnts.tsv"
     if args.assign_pops or args.run:
-        predict_pops(pca_scores_file, pop_ht_file, pop_ht_tsv)
-
+        predict_pops(config)
 
 if __name__ == '__main__':
-    main() 
\ No newline at end of file
+    main() 
diff --git a/2-sample_qc/4-find_population_outliers.py b/2-sample_qc/4-find_population_outliers.py
index d2c320a..ac4ce25 100644
--- a/2-sample_qc/4-find_population_outliers.py
+++ b/2-sample_qc/4-find_population_outliers.py
@@ -1,47 +1,74 @@
 # perform hail sample QC stratified by superpopulation and identify outliers
 import hail as hl
 import pyspark
-from utils.utils import parse_config
+import os.path
+from utils.utils import parse_config, path_local, path_spark
 from gnomad.sample_qc.filtering import compute_stratified_metrics_filter
 
-
-def annotate_mt(raw_mt_file: str, pop_ht_file: str, annotated_mt_file: str, pop_pandas_file: str):
+# TODO: rename to annotate_with_pop
+def annotate_mt(raw_mt_file: str, pop_ht_file: str, annotated_mt_file: str, config: dict = None):
     '''
     Annotate mt with superpopulation and sequencing runid
     :param str raw_mt_file: raw mt file
     :param str pop_ht_file: file with population annotations
-    :param str runid_file: metadata file to annotate run ids
+    :param str runid_file: metadata file to annotate run ids TODO
     :param str annotated_mt_file: annotated mt file
     :param str pop_pandas_file: tsv from pandas df - EGA and pop
+    :param dict config: A config object. No effect.
+
+    ### Config fields
+    None
+
+    ### Indirect config fields
+    step1.gatk_mt_outfile : input path : used in main   
+    step2.predict_populations.pop_ht_file : input path : used in main  
+    step2.annotate_with_pop.annotated_mt_file : output path : used in main  
     '''
-    mt = hl.read_matrix_table(raw_mt_file)
-    #pop_ht = hl.read_table(pop_ht_file)
-    pop_ht = hl.import_table(pop_pandas_file, delimiter="\t").key_by('s')
+    mt = hl.read_matrix_table(path_spark(raw_mt_file))
+    pop_ht = hl.read_table(path_spark(pop_ht_file))
     mt = mt.annotate_cols(assigned_pop=pop_ht[mt.s].pop)
-    mt.write(annotated_mt_file, overwrite=True)
+    mt.write(path_spark(annotated_mt_file), overwrite=True) # output
+    return mt
 
 
-def stratified_sample_qc(annotated_mt_file: str, mt_qc_outfile: str, ht_qc_cols_outfile: str, qc_filter_file: str, annotdir: str):
+def stratified_sample_qc(annotated_mt_file: str, mt_qc_outfile: str, ht_qc_cols_outfile: str, qc_filter_file: str, config: dict):
     '''
     Run sample QC and stratify by population
     param str annotated_mt_file: population and run id annotated MT file
     param str mt_qc_outfile: sample QC MT file
     param str ht_qccols_outfile: sample QC columns HT file
     param str qc_filter_file: output file for stratified sample QC HT
-    param str annotdir: output directory for annotations
+    param dict config: config object
+
+    TODO: note about `if min_dp > 0 or min_gq > 0 or min_vaf > 0`
+
+    ### Config fields 
+    step2.stratified_sample_qc.min_dp : float : TODO   
+    step2.stratified_sample_qc.min_gq : float : TODO   
+    step2.stratified_sample_qc.min_vaf : float : TODO   
+    step2.stratified_sample_qc.output_text_file : output path : TODO   
+    step2.stratified_sample_qc.output_globals_json_file : output path : TODO   
+
+    ### Indirect config fields
+    step2.annotate_with_pop.annotated_mt_file : input path : used in main  
+    step2.stratified_sample_qc.mt_qc_outfile : output path : used in main   
+    step2.stratified_sample_qc.ht_qc_cols_outfile : output path : used in main   
+    step2.stratified_sample_qc.qc_filter_file : output path : used in main  
     '''
-    mt = hl.read_matrix_table(annotated_mt_file)
+    conf = config['step2']['stratified_sample_qc']
+
+    mt = hl.read_matrix_table(path_spark(annotated_mt_file))
     # filter to autosomes only
     mt = mt.filter_rows(mt.locus.in_autosome())
 
     # filter MT by depth/gq/vaf
-    min_dp = 20
-    min_gq = 20
-    min_vaf = 0.25
+
+    min_dp = conf['min_depth']
+    min_gq = conf['min_genotype_quality']
+    min_vaf = conf['min_vaf']
     if min_dp > 0 or min_gq > 0 or min_vaf > 0:
         vaf = mt.AD[1] / hl.sum(mt.AD)
-        print("Filtering input MT by depth: DP=" + str(min_dp) +
-              ", genotype quality: GQ=" + str(min_gq) + ", VAF: VAF=" + str(min_vaf))
+        print(f"Filtering input MT by depth: DP={min_dp}, genotype quality: GQ={min_gq}, VAF: VAF={min_vaf}")
         filter_condition = ((mt.GT.is_het() & (vaf > min_vaf) & (mt.DP > min_dp) & (mt.GQ > min_gq)) |
                             (mt.GT.is_hom_ref() & (mt.DP > min_dp) & (mt.GQ > min_gq)) |
                             (mt.GT.is_hom_var() & (mt.DP > min_dp) & (mt.GQ > min_gq)))
@@ -56,84 +83,69 @@ def stratified_sample_qc(annotated_mt_file: str, mt_qc_outfile: str, ht_qc_cols_
     # annotate with heterozygosity rate
     mt_with_sampleqc = mt_with_sampleqc.annotate_cols(sample_qc=mt_with_sampleqc.sample_qc.annotate(
         heterozygosity_rate=mt_with_sampleqc.sample_qc.n_het/mt_with_sampleqc.sample_qc.n_called))
-    mt_with_sampleqc.write(mt_qc_outfile, overwrite=True)
-    mt_with_sampleqc.cols().write(ht_qc_cols_outfile,  overwrite=True)
+    
+    mt_with_sampleqc.write(path_spark(mt_qc_outfile), overwrite=True) # output
+    mt_with_sampleqc.cols().write(path_spark(ht_qc_cols_outfile),  overwrite=True) # output
+
     # stratify by pop
-    pop_ht = hl.read_table(ht_qc_cols_outfile)
+    pop_ht = hl.read_table(path_spark(ht_qc_cols_outfile))
+    # TODO: shall we move qc_metrics to the config?
     qc_metrics = ['heterozygosity_rate', 'n_snp', 'r_ti_tv', 'n_transition', 'n_transversion',
                   'r_insertion_deletion', 'n_insertion', 'n_deletion', 'r_het_hom_var']
 
-    pop_ht_afr = pop_ht.filter(pop_ht.assigned_pop == 'AFR')
-    pop_ht_nonafr = pop_ht.filter(pop_ht.assigned_pop != 'AFR')
-
-    pop_filter_ht_afr = compute_stratified_metrics_filter(
-        pop_ht_afr,
+    pop_filter_ht = compute_stratified_metrics_filter(
+        pop_ht,
         qc_metrics={
-            metric: pop_ht_afr.sample_qc[metric] for metric in qc_metrics
+            metric: pop_ht.sample_qc[metric] for metric in qc_metrics
         },
-        metric_threshold={'heterozygosity_rate': (100, 4),
-                          'r_het_hom_var': (100, 5)},
-
-        strata={"qc_pop": pop_ht_afr.assigned_pop},
+        strata={"qc_pop": pop_ht.assigned_pop},
     )
 
-    pop_filter_ht_nonafr = compute_stratified_metrics_filter(
-        pop_ht_nonafr,
-        qc_metrics={
-            metric: pop_ht_nonafr.sample_qc[metric] for metric in qc_metrics
-        },
-        metric_threshold={'heterozygosity_rate': (100, 4),
-                          'r_het_hom_var': (100, 4)},
+    globals = hl.eval(pop_filter_ht.globals.qc_metrics_stats)
 
-        strata={"qc_pop": pop_ht_nonafr.assigned_pop},
-    )
-
-    pop_filter_ht = pop_filter_ht_afr.union(pop_filter_ht_nonafr)
-    globals1 = hl.eval(pop_filter_ht_nonafr.globals.qc_metrics_stats)
-    globals2 = hl.eval(pop_filter_ht_afr.globals.qc_metrics_stats)
-    globals1.update(globals2)
-
-    pop_ht = pop_ht.annotate_globals(qc_metrics_stats=globals1)
+    pop_ht = pop_ht.annotate_globals(qc_metrics_stats=globals)
     pop_ht = pop_ht.annotate(**pop_filter_ht[pop_ht.key]).persist()
     checkpoint = pop_ht.aggregate(hl.agg.count_where(
-        hl.len(pop_ht.qc_metrics_filters) == 0))
+        hl.len(pop_ht.qc_metrics_filters) == 0)
+    )
     print(f'{checkpoint} exome samples found passing pop filtering')
-    pop_ht.write(qc_filter_file, overwrite=True)
+    pop_ht.write(path_spark(qc_filter_file), overwrite=True) # output
 
-    output_text_file = annotdir + "sample_qc_by_pop.tsv.bgz"
-    pop_ht.export(output_text_file, delimiter="\t")
+    # output_text_file = os.path.join(annotdir, "sample_qc_by_pop.tsv.bgz")
+    output_text_file = conf['output_text_file']
+    pop_ht.export(path_spark(output_text_file), delimiter="\t") # output
 
-    output_globals_json = annotdir + "sample_qc_by_pop.globals.json"
-    pop_ht.globals.export(output_globals_json)
+    # output_globals_json = os.path.join(annotdir, "sample_qc_by_pop.globals.json")
+    output_globals_json = conf['output_globals_json_file']
+    pop_ht.globals.export(path_spark(output_globals_json)) # output
 
 
 def main():
     # set up
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
-    annotdir = inputs['annotation_lustre_dir']
-    resourcesdir = inputs['resource_dir']
-    #mtdir2 = inputs['load_matrixtables_lustre_dir']
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
+    annotdir = config['general']['annotation_dir']
+    resourcesdir = config['general']['resource_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
     # annotate mt with runid and pop
-    raw_mt_file = mtdir + "gatk_unprocessed.mt"
-    pop_ht_file = mtdir + "pop_assignments.ht"
-    annotated_mt_file = mtdir + "gatk_unprocessed_with_pop.mt"
-    pop_pandas_file = mtdir + "pop_assignemtnts.tsv"
-    annotate_mt(raw_mt_file, pop_ht_file, annotated_mt_file, pop_pandas_file)
+    raw_mt_file = config['step1']['gatk_mt_outfile']
+    pop_ht_file = config['step2']['predict_pops']['pop_ht_outfile']
+    pop_ht_tsv = config['step2']['predict_pops']['pop_ht_outtsv']
+    annotated_mt_file = config['step2']['annotate_with_pop']['annotated_mt_file']
+    annotate_mt(raw_mt_file, pop_ht_file, annotated_mt_file)
 
     # run sample QC and stratify by population
-    mt_qc_outfile = mtdir + "mt_pops_sampleqc.mt"
-    ht_qc_cols_outfile = mtdir + "mt_pops_sampleqc.ht"
-    qc_filter_file = mtdir + "mt_pops_QC_filters.ht"
+    mt_qc_outfile = config['step2']['stratified_sample_qc']['mt_qc_outfile']
+    ht_qc_cols_outfile = config['step2']['stratified_sample_qc']['ht_qc_cols_outfile']
+    qc_filter_file = config['step2']['stratified_sample_qc']['qc_filter_file']
     stratified_sample_qc(annotated_mt_file, mt_qc_outfile,
-                         ht_qc_cols_outfile, qc_filter_file, annotdir)
+                         ht_qc_cols_outfile, qc_filter_file, config)
 
 
 if __name__ == '__main__':
diff --git a/2-sample_qc/5-filter_fail_sample_qc.py b/2-sample_qc/5-filter_fail_sample_qc.py
index 35e2f1e..fc7e8a0 100644
--- a/2-sample_qc/5-filter_fail_sample_qc.py
+++ b/2-sample_qc/5-filter_fail_sample_qc.py
@@ -2,8 +2,10 @@
 # Filter to remove samples sequenced at Broad
 import hail as hl
 import pyspark
-from utils.utils import parse_config
+import os
+from utils.utils import parse_config, path_spark, path_local
 
+# TODO: not used? make it optional and mention in cli help
 def filter_to_sanger_only(annotated_mt_file: str, sanger_mt_file: str):
     '''
     param str annotated_mt_file: File containing MatrixTable annotated with sequencing location
@@ -17,15 +19,25 @@ def filter_to_sanger_only(annotated_mt_file: str, sanger_mt_file: str):
     mt.write(sanger_mt_file)
 
 
-def remove_sample_qc_fails(sanger_mt_file: str, qc_filter_ht_file: str, samples_failing_qc_file: str, sample_qc_filtered_mt_file: str):
+def remove_sample_qc_fails(mt_file: str, qc_filter_ht_file: str, samples_failing_qc_file: str, sample_qc_filtered_mt_file: str, config: dict = None):
     '''
-    param str sanger_mt_file: Input MatrixTable file
+    param str mt_file: Input MatrixTable file
     param str qc_filter_ht_file: File contaning sample QC output
     param str samples_failing_qc_file: Output file for list of samples failing QC
     param str sample_qc_filtered_mt_file: Output file for MatrixTable with sample QC fails removed
+    param dict config: A config object. No effect.
+
+    ### Config fields
+    None
+
+    ### Indirect config fields
+    step2.annotate_with_pop.annotated_mt_file : input path : used in main   
+    step2.stratified_sample_qc.mt_qc_outfile : input path : used in main   
+    step2.remove_sample_qc_fails.samples_failing_qc_file : output path : used in main   
+    step2.remove_sample_qc_fails.sample_qc_filtered_mt_file : output path : used in main   
     '''
-    sangermt = hl.read_matrix_table(sanger_mt_file)
-    sample_qc_ht = hl.read_table(qc_filter_ht_file)
+    mt = hl.read_matrix_table(path_spark(mt_file))
+    sample_qc_ht = hl.read_table(path_spark(qc_filter_ht_file))
     # identify samples which have failed any of the metrics tested
     sample_qc_ht = sample_qc_ht.annotate(filter_fail_count=(hl.len(sample_qc_ht.qc_metrics_filters)))
 
@@ -38,30 +50,37 @@ def remove_sample_qc_fails(sanger_mt_file: str, qc_filter_ht_file: str, samples_
     # save a list of samples that have failed QC
     fail_ht = sample_qc_ht.filter(sample_qc_ht.filter_result == 'Fail').key_by()
     fails = fail_ht.select(fail_ht.s)
-    fails.export(samples_failing_qc_file)
+    fails.export(path_spark(samples_failing_qc_file)) # output
     # filter the sangermt to remove samples that have failed
     fails = fails.key_by('s')
-    sangermt = sangermt.filter_cols(hl.is_defined(fails[sangermt.s]), keep=False)
+    mt = mt.filter_cols(hl.is_defined(fails[mt.s]), keep=False)
     # save the filtered mt to file
-    sangermt.write(sample_qc_filtered_mt_file, overwrite=True)
+    mt.write(path_spark(sample_qc_filtered_mt_file), overwrite=True) # output
 
 
 def main():
     # set up
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
-    annotdir = inputs['annotation_lustre_dir']
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
+    annotdir = config['general']['annotation_dir']
+    resourcesdir = config['general']['resource_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    # tmp_dir = "file:///lustre/scratch126/dh24_test/tmp"
+    tmp_dir = config['general']['tmp_dir']
+    # sc = pyspark.SparkContext()
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
-    qc_filter_ht_file = mtdir + "mt_pops_QC_filters.ht"
-    annotated_mt_file = mtdir + "gatk_unprocessed_with_pop.mt"  # annotated but unfiltered mt
-    sample_qc_filtered_mt_file = mtdir + "mt_pops_QC_filters_after_sample_qc.mt"
-    samples_failing_qc_file = annotdir + "samples_failing_qc.tsv.bgz"
+    # annotated_mt_file = os.path.join(mtdir,"gatk_unprocessed_with_pop.mt")  # annotated but unfiltered mt
+    # qc_filter_ht_file = os.path.join(mtdir,"mt_pops_QC_filters.ht")
+    # samples_failing_qc_file = os.path.join(annotdir, "samples_failing_qc.tsv.bgz")
+    # sample_qc_filtered_mt_file = os.path.join(mtdir,"mt_pops_QC_filters_after_sample_qc.mt")
+    annotated_mt_file = config['step2']['annotate_with_pop']['annotated_mt_file'] # annotated but unfiltered mt
+    qc_filter_ht_file = config['step2']['stratified_sample_qc']['qc_filter_file']
+    samples_failing_qc_file = config['step2']['remove_sample_qc_fails']['samples_failing_qc_file']
+    sample_qc_filtered_mt_file = config['step2']['remove_sample_qc_fails']['sample_qc_filtered_mt_file']
     remove_sample_qc_fails(annotated_mt_file, qc_filter_ht_file, samples_failing_qc_file, sample_qc_filtered_mt_file)
 
 
diff --git a/3-variant_qc/1-generate_truth_sets.py b/3-variant_qc/1-generate_truth_sets.py
index bc91e99..443ed26 100644
--- a/3-variant_qc/1-generate_truth_sets.py
+++ b/3-variant_qc/1-generate_truth_sets.py
@@ -1,9 +1,10 @@
 # generate truth sets for variant QC random forest
 import hail as hl
+import hailtop.fs as hfs
 import pyspark
 import argparse
 from typing import Tuple
-from utils.utils import parse_config, rm_mt
+from utils.utils import parse_config, rm_mt, path_spark, path_local
 from gnomad.utils.filtering import filter_to_adj, filter_to_autosomes
 from gnomad.utils.annotations import unphase_call_expr, bi_allelic_site_inbreeding_expr, add_variant_type, annotate_adj, bi_allelic_expr
 from gnomad.sample_qc.relatedness import generate_trio_stats_expr
@@ -28,7 +29,7 @@ def get_options():
     return args
 
 
-def get_truth_ht(omni, mills, thousand_genomes, hapmap, truth_ht_file):
+def get_truth_ht(omni: str, mills: str, thousand_genomes: str, hapmap: str, truth_ht_file: str) -> None:
     '''
     Generate truth set HT
     :param str omni: file containing kgp_omni 1000 Genomes intersection Onni 2.5M array
@@ -37,19 +38,19 @@ def get_truth_ht(omni, mills, thousand_genomes, hapmap, truth_ht_file):
     :param str hapmap: file containing hapmap
     :param str truth_ht_file: output file name
     '''
-    omni_ht = hl.read_table(omni)
-    mills_ht = hl.read_table(mills)
-    thousand_genomes_ht = hl.read_table(thousand_genomes)
-    hapmap_ht = hl.read_table(hapmap)
+    omni_ht = hl.read_table(path_spark(omni))
+    mills_ht = hl.read_table(path_spark(mills))
+    thousand_genomes_ht = hl.read_table(path_spark(thousand_genomes))
+    hapmap_ht = hl.read_table(path_spark(hapmap))
 
     truth_ht = hapmap_ht.select(hapmap=True).join(
         omni_ht.select(omni=True), how="outer").join(
             thousand_genomes_ht.select(kgp_phase1_hc=True), how="outer").join(
-                mills_ht.select(mills=True), how="outer").repartition(200, shuffle=False)
+                mills_ht.select(mills=True), how="outer").repartition(200, shuffle=False) # TODO: I suppose this number should not be considered as a config parameter candidate, should it?
     truth_ht.write(truth_ht_file, overwrite=True)
     
 
-def split_multi_and_var_qc(mtfile: str, varqc_mtfile: str, varqc_mtfile_split: str):
+def split_multi_and_var_qc(mtfile: str, varqc_mtfile: str, varqc_mtfile_split: str) -> None:
     '''
     Adapted from https://github.com/broadinstitute/gnomad_qc/blob/3d79bdf0f7049c209b4659ff8c418a1b859d7cfa/gnomad_qc/v2/annotations/generate_qc_annotations.py
     Run split_multi_hts and variant QC on inout mt after sample QC
@@ -57,7 +58,7 @@ def split_multi_and_var_qc(mtfile: str, varqc_mtfile: str, varqc_mtfile_split: s
     :param str varqc_mtfile: Output mt with adj annotation 
     :param str varqc_mtfile_split: Output mt with variant QC annotation and split multiallelics
     '''
-    mt = hl.read_matrix_table(mtfile)
+    mt = hl.read_matrix_table(path_spark(mtfile))
 
     #        # restrict to samples in trios
     # samplefile = "file:///lustre/scratch123/qc/resources/samples_in_trios.txt"
@@ -68,10 +69,10 @@ def split_multi_and_var_qc(mtfile: str, varqc_mtfile: str, varqc_mtfile_split: s
     #before splitting annotate with sum_ad
     mt = mt.annotate_entries(sum_AD = hl.sum(mt.AD))
     mt = annotate_adj(mt)
-    mt = mt.checkpoint(varqc_mtfile, overwrite=True)
+    mt = mt.checkpoint(path_spark(varqc_mtfile), overwrite=True)
 
     mt = hl.split_multi_hts(mt)
-    tmp_mt = varqc_mtfile_split + "_tmp"
+    tmp_mt = path_spark(varqc_mtfile_split + "_tmp")
     print("writing split mt")
     mt = mt.checkpoint(tmp_mt, overwrite=True)
 
@@ -107,8 +108,10 @@ def split_multi_and_var_qc(mtfile: str, varqc_mtfile: str, varqc_mtfile_split: s
     )
 
     print("writing split mt")
-    mt.write(varqc_mtfile_split, overwrite=True)
-    rm_mt(tmp_mt)
+    mt.write(path_spark(varqc_mtfile_split), overwrite=True)
+    # rm_mt(tmp_mt) # DEBUG: this doesn't work for me
+    hfs.rmtree(tmp_mt)
+
 
 
 def read_fam(fam_file: str) -> hl.Table:
@@ -116,14 +119,14 @@ def read_fam(fam_file: str) -> hl.Table:
     Taken from https://github.com/broadinstitute/gnomad_qc/blob/3d79bdf0f7049c209b4659ff8c418a1b859d7cfa/gnomad_qc/v2/annotations/generate_qc_annotations.py
     '''
     columns = ['fam_id', 's', 'pat_id', 'mat_id', 'is_female']
-    return hl.import_table(fam_file, no_header=True).rename({f'f{i}': c for i, c in enumerate(columns)}).key_by('s')
+    return hl.import_table(path_spark(fam_file), no_header=True).rename({f'f{i}': c for i, c in enumerate(columns)}).key_by('s')
 
 
 def annotate_unrelated_sample(mt: hl.MatrixTable, fam_file: str) -> hl.MatrixTable:
     '''
     Taken from https://github.com/broadinstitute/gnomad_qc/blob/3d79bdf0f7049c209b4659ff8c418a1b859d7cfa/gnomad_qc/v2/annotations/generate_qc_annotations.py
     '''
-    fam_ht = read_fam(fam_file)
+    fam_ht = read_fam(path_spark(fam_file))
     return mt.annotate_cols(unrelated_sample=hl.is_missing(fam_ht[mt.s]))
 
 
@@ -159,7 +162,7 @@ def generate_family_stats(mt: hl.MatrixTable, fam_file: str, calculate_adj: bool
 
     # Unphased for now, since mendel_errors does not support phased alleles
     mt = mt.annotate_entries(GT=unphase_call_expr(mt.GT))
-    ped = hl.Pedigree.read(fam_file, delimiter='\\t')
+    ped = hl.Pedigree.read(path_spark(fam_file), delimiter='\\t')
     family_stats_struct, family_stats_sample_ht = family_stats(mt, ped, 'raw')
     mt = mt.annotate_rows(family_stats=[family_stats_struct])
 
@@ -210,7 +213,9 @@ def generate_trio_stats(
     return ht
 
 
-def trio_family_dnm_annotation(varqc_mtfile: str, pedfile: str, trio_mtfile: str, trio_stats_htfile: str, fam_stats_htfile: str, fam_stats_mtfile: str, fam_stats_gnomad_mtfile: str, gnomad_htfile: str, dnm_htfile: str):
+def trio_family_dnm_annotation(varqc_mtfile: str, pedfile: str, trio_mtfile: str, 
+                               trio_stats_htfile: str, fam_stats_htfile: str, fam_stats_mtfile: str, 
+                               fam_stats_gnomad_mtfile: str, gnomad_htfile: str, dnm_htfile: str) -> None:
     '''
     Create matrixtable of just trios, create family stats
     :param str varqc_mtfile: Input matrixtable file
@@ -223,35 +228,35 @@ def trio_family_dnm_annotation(varqc_mtfile: str, pedfile: str, trio_mtfile: str
     :param str gnomad_htfile: Gnomad AF hail table
     :param str dnm_htfile: De novo hail table file
     '''
-    pedigree = hl.Pedigree.read(pedfile)
-    mt = hl.read_matrix_table(varqc_mtfile)
+    pedigree = hl.Pedigree.read(path_spark(pedfile))
+    mt = hl.read_matrix_table(path_spark(varqc_mtfile))
 
     #filter mt to samples that are in trios only and re-run varqc
-    trio_sample_ht = hl.import_fam(pedfile)
+    trio_sample_ht = hl.import_fam(path_spark(pedfile))
     sample_list = trio_sample_ht.id.collect() + trio_sample_ht.pat_id.collect() + trio_sample_ht.mat_id.collect()
     mt2 = mt.filter_cols(hl.set(sample_list).contains(mt.s))
     mt2 = hl.variant_qc(mt2, name = 'varqc_trios')
 
     trio_dataset = hl.trio_matrix(mt2, pedigree, complete_trios=True)
-    trio_dataset.write(trio_mtfile, overwrite=True)
+    trio_dataset.write(path_spark(trio_mtfile), overwrite=True)
 
     trio_stats_ht = generate_trio_stats(trio_dataset, autosomes_only=True, bi_allelic_only=False)
-    trio_stats_ht.write(trio_stats_htfile, overwrite=True)
+    trio_stats_ht.write(path_spark(trio_stats_htfile), overwrite=True)
 
     print("Generating family stats")
     (ht1, famstats_ht) = generate_family_stats(mt, pedfile)
-    ht1.write(fam_stats_htfile ,overwrite=True)
+    ht1.write(path_spark(fam_stats_htfile), overwrite=True)
 
     mt = mt.annotate_rows(family_stats=ht1[mt.row_key].family_stats)
-    mt = mt.checkpoint(fam_stats_mtfile, overwrite=True)
+    mt = mt.checkpoint(path_spark(fam_stats_mtfile), overwrite=True)
     #add gnomad AFs
-    gnomad_ht = hl.read_table(gnomad_htfile)
+    gnomad_ht = hl.read_table(path_spark(gnomad_htfile))
     mt = mt.annotate_rows(gnomad_maf=gnomad_ht[mt.row_key].freq[0].AF)
-    mt.write(fam_stats_gnomad_mtfile, overwrite=True)
+    mt.write(path_spark(fam_stats_gnomad_mtfile), overwrite=True)
     #make DNM table
     de_novo_table = hl.de_novo(mt, pedigree, mt.gnomad_maf)
     de_novo_table = de_novo_table.key_by('locus', 'alleles').collect_by_key('de_novo_data')
-    de_novo_table.repartition(480).write(dnm_htfile, overwrite=True)
+    de_novo_table.repartition(480).write(path_spark(dnm_htfile), overwrite=True)
 
     rm_mt(fam_stats_mtfile)
 
@@ -288,7 +293,7 @@ def generate_ac(mt: hl.MatrixTable, fam_file: str) -> hl.Table:
     Creates Table with QC samples, QC samples removing children and release samples raw and adj ACs.
     """
     # mt = mt.filter_cols(mt.meta.high_quality)
-    fam_ht = hl.import_fam(fam_file, delimiter="\t")
+    fam_ht = hl.import_fam(path_spark(fam_file), delimiter="\t")
     mt = mt.annotate_cols(unrelated_sample=hl.is_missing(fam_ht[mt.s]))
     mt = mt.filter_rows(hl.len(mt.alleles) > 1)
     mt = mt.annotate_rows(
@@ -308,7 +313,7 @@ def create_inbreeding_ht_with_ac_and_allele_data(varqc_mtfile: str, pedfile: str
     :param str qc_ac_htfile: qc_ac hail table file
     :param str allele_data_htfile: Allele data htfile
     '''
-    mt = hl.read_matrix_table(varqc_mtfile)
+    mt = hl.read_matrix_table(path_spark(varqc_mtfile))
     # inbreeding ht
     mt_inbreeding = mt.annotate_rows(InbreedingCoeff=bi_allelic_site_inbreeding_expr(mt.GT))
     #mt = mt.key_rows_by('locus').distinct_by_row().key_rows_by('locus', 'alleles')
@@ -317,58 +322,58 @@ def create_inbreeding_ht_with_ac_and_allele_data(varqc_mtfile: str, pedfile: str
     allele_data_ht = generate_allele_data(mt)
     qc_ac_ht = generate_ac(mt, pedfile)
     # write to file
-    ht_inbreeding.write(inbreeding_htfile , overwrite=True)
-    qc_ac_ht.write(qc_ac_htfile , overwrite=True)
-    allele_data_ht.write(allele_data_htfile, overwrite=True)
+    ht_inbreeding.write(path_spark(inbreeding_htfile), overwrite=True)
+    qc_ac_ht.write(path_spark(qc_ac_htfile), overwrite=True)
+    allele_data_ht.write(path_spark(allele_data_htfile), overwrite=True)
 
 
 def main():
-    #set up
+    # set up
     args = get_options()
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
-    resourcedir = inputs['resource_dir']
-    training_sets_dir = inputs['training_set_dir']
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
+    resourcedir = config['general']['resource_dir']
+    training_sets_dir = config['general']['training_sets_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
     # get truth set ht
-    truth_ht_file = resourcedir + "truthset_table.ht"
     if args.truth or args.all:
-        omni = training_sets_dir + "1000G_omni2.5.hg38.ht"
-        mills = training_sets_dir + "Mills_and_1000G_gold_standard.indels.hg38.ht"
-        thousand_genomes = training_sets_dir + "1000G_phase1.snps.high_confidence.hg38.ht"
-        hapmap = training_sets_dir + "hapmap_3.3.hg38.ht"
-        get_truth_ht(omni, mills, thousand_genomes, hapmap, truth_ht_file)
+        truth_ht_outfile = config['step3']['get_truth_ht']['truth_ht_outfile']
+        omni = config['step3']['get_truth_ht']['omni']
+        mills = config['step3']['get_truth_ht']['mills']
+        thousand_genomes = config['step3']['get_truth_ht']['thousand_genomes']
+        hapmap = config['step3']['get_truth_ht']['hapmap']
+        get_truth_ht(omni, mills, thousand_genomes, hapmap, truth_ht_outfile)
 
     #add hail variant QC
     if args.annotation or args.all:
-        mtfile = mtdir + "mt_pops_QC_filters_after_sample_qc.mt"
-        varqc_mtfile = mtdir + "mt_varqc.mt"
-        varqc_mtfile_split = mtdir + "mt_varqc_splitmulti.mt"
+        mtfile = config['step3']['split_multi_and_var_qc']['mtfile']
+        varqc_mtoutfile = config['step3']['split_multi_and_var_qc']['varqc_mtoutfile']
+        varqc_mtoutfile_split = config['step3']['split_multi_and_var_qc']['varqc_mtoutfile_split']
 
-        split_multi_and_var_qc(mtfile, varqc_mtfile, varqc_mtfile_split)
-        pedfile = "file:///lustre/scratch123/qc/BiB/trios.EGAN.complete.ped"
+        split_multi_and_var_qc(mtfile, varqc_mtoutfile, varqc_mtoutfile_split)
+        pedfile = config['step3']['pedfile']
 
         #get complete trios, family annotation, dnm annotation
-        trio_mtfile = mtdir + "trios.mt"
-        trio_stats_htfile = mtdir + "trio_stats.ht"
-        fam_stats_htfile = mtdir + "family_stats.ht"
-        fam_stats_mtfile = mtdir + "family_stats.mt"
-        fam_stats_gnomad_mtfile = mtdir + "family_stats_gnomad.mt"
-        gnomad_htfile = resourcedir + "gnomad.exomes.r2.1.1.sites.liftover_grch38.ht"
-        dnm_htfile = mtdir + "denovo_table.ht"
-        trio_family_dnm_annotation(varqc_mtfile_split, pedfile, trio_mtfile, trio_stats_htfile, fam_stats_htfile, fam_stats_mtfile, fam_stats_gnomad_mtfile, gnomad_htfile, dnm_htfile)
+        trio_mtoutfile = config['step3']['trio_family_dnm_annotation']['trio_mtoutfile']
+        trio_stats_htoutfile = config['step3']['trio_family_dnm_annotation']['trio_stats_htoutfile']
+        fam_stats_htoutfile = config['step3']['trio_family_dnm_annotation']['fam_stats_htoutfile']
+        fam_stats_mtoutfile = config['step3']['trio_family_dnm_annotation']['fam_stats_mtoutfile']
+        fam_stats_gnomad_mtoutfile = config['step3']['trio_family_dnm_annotation']['fam_stats_gnomad_mtoutfile']
+        gnomad_htfile = config['step3']['trio_family_dnm_annotation']['gnomad_htfile']
+        dnm_htoutfile = config['step3']['trio_family_dnm_annotation']['dnm_htoutfile']
+        trio_family_dnm_annotation(varqc_mtoutfile_split, pedfile, trio_mtoutfile, trio_stats_htoutfile, fam_stats_htoutfile, fam_stats_mtoutfile, fam_stats_gnomad_mtoutfile, gnomad_htfile, dnm_htoutfile)
 
         #create inbreeding ht
-        inbreeding_htfile = mtdir + "inbreeding.ht"
-        qc_ac_htfile = mtdir + "qc_ac.ht"
-        allele_data_htfile = mtdir + "allele_data.ht"
-        create_inbreeding_ht_with_ac_and_allele_data(varqc_mtfile, pedfile, inbreeding_htfile, qc_ac_htfile, allele_data_htfile)
+        inbreeding_htoutfile = config['step3']['create_inbreeding_ht_with_ac_and_allele_data']['inbreeding_htoutfile']
+        qc_ac_htoutfile = config['step3']['create_inbreeding_ht_with_ac_and_allele_data']['qc_ac_htoutfile']
+        allele_data_htoutfile = config['step3']['create_inbreeding_ht_with_ac_and_allele_data']['allele_data_htoutfile']
+        create_inbreeding_ht_with_ac_and_allele_data(varqc_mtoutfile, pedfile, inbreeding_htoutfile, qc_ac_htoutfile, allele_data_htoutfile)
 
 
 if __name__ == '__main__':
diff --git a/3-variant_qc/2-create_rf_ht.py b/3-variant_qc/2-create_rf_ht.py
index 663158d..55ba0a7 100755
--- a/3-variant_qc/2-create_rf_ht.py
+++ b/3-variant_qc/2-create_rf_ht.py
@@ -1,12 +1,14 @@
-#create hail table for random forest
+# create hail table for random forest
 import hail as hl
 import pyspark
 import utils.constants as constants
-from utils.utils import parse_config
+from utils.utils import parse_config, path_spark, path_local
 from gnomad.variant_qc.random_forest import median_impute_features
 
 
-def create_rf_ht(mtfile: str, truthset_file: str, trio_stats_file: str, allele_data_file: str, allele_counts_file: str, inbreeding_file: str, htfile_rf_all_cols: str, htfile_rf_var_type_all_cols: str):
+def create_rf_ht(mtfile: str, truthset_file: str, trio_stats_file: str, allele_data_file: str, 
+                 allele_counts_file: str, inbreeding_file: str, 
+                 htfile_rf_all_cols: str, htfile_rf_var_type_all_cols: str, config: dict) -> None:
     '''
     Load input mt and training data to create an input for random forest
     param str mtfile: Input matrixtable file
@@ -18,13 +20,15 @@ def create_rf_ht(mtfile: str, truthset_file: str, trio_stats_file: str, allele_d
     param str htfile_rf_all_cols: Output file for RF hail table 
     param str htfile_rf_var_type_all_cols: Output file for RF hail table by variant type
     '''
+    conf = config['step3']['create_rf_ht']
+
     n_partitions = 200
-    mt = hl.read_matrix_table(mtfile)
-    truth_data_ht = hl.read_table(truthset_file)
-    trio_stats_table = hl.read_table(trio_stats_file)
-    allele_data_ht = hl.read_table(allele_data_file)
-    allele_counts_ht = hl.read_table(allele_counts_file)
-    inbreeding_ht = hl.read_table(inbreeding_file)
+    mt = hl.read_matrix_table(path_spark(mtfile))
+    truth_data_ht = hl.read_table(path_spark(truthset_file))
+    trio_stats_table = hl.read_table(path_spark(trio_stats_file))
+    allele_data_ht = hl.read_table(path_spark(allele_data_file))
+    allele_counts_ht = hl.read_table(path_spark(allele_counts_file))
+    inbreeding_ht = hl.read_table(path_spark(inbreeding_file))
 
     allele_counts_ht = allele_counts_ht.select(*['ac_qc_samples_raw', 'ac_qc_samples_adj'])
     group = "raw"
@@ -56,12 +60,13 @@ def create_rf_ht(mtfile: str, truthset_file: str, trio_stats_file: str, allele_d
     # ht = ht.annotate(is_CG=((ht.alleles[0] == "C") & (ht.alleles[1] == "G")) | ((ht.alleles[0] == "G") & (ht.alleles[1] == "C")))
     # ht = ht.annotate(is_CT=((ht.alleles[0] == "C") & (ht.alleles[1] == "T")) | ((ht.alleles[0] == "G") & (ht.alleles[1] == "A")))
 
-    ht = ht.annotate(fail_hard_filters=(ht.QD < 2)
-                     | (ht.FS > 60) | (ht.MQ < 30))
+    ht = ht.annotate(fail_hard_filters=(ht.QD < conf['fail_hard_filters_QD_less_than'])
+                     | (ht.FS > conf['fail_hard_filters_FS_greater_than']) | (ht.MQ < conf['fail_hard_filters_MQ_less_than']))
     ht = ht.annotate(ac_raw=ht.ac_qc_samples_raw)
     ht = ht.annotate(transmitted_singleton=(
         ht[f"n_transmitted_{group}"] == 1) & (ht[f"ac_qc_samples_{group}"] == 2))
 
+    # TODO: are these thresholds separate from the ones above?
     ht = ht.select(
         "a_index",
         # "was_split",
@@ -70,41 +75,45 @@ def create_rf_ht(mtfile: str, truthset_file: str, trio_stats_file: str, allele_d
         **{
             "transmitted_singleton": (ht[f"n_transmitted_{group}"] == 1)
             & (ht[f"ac_qc_samples_{group}"] == 2),
-            "fail_hard_filters": (ht.QD < 2) | (ht.FS > 60) | (ht.MQ < 30),
+            "fail_hard_filters": (ht.QD < conf['fail_hard_filters_QD_less_than']) 
+            | (ht.FS > conf['fail_hard_filters_FS_greater_than']) | (ht.MQ < conf['fail_hard_filters_MQ_less_than']),
         },
         ac_raw=ht.ac_qc_samples_raw
     )
 
     ht = ht.repartition(n_partitions, shuffle=False)
-    ht = ht.checkpoint(htfile_rf_all_cols, overwrite=True)
+    ht = ht.checkpoint(path_spark(htfile_rf_all_cols), overwrite=True)
     ht = median_impute_features(ht, strata={"variant_type": ht.variant_type})
-    ht.write(htfile_rf_var_type_all_cols, overwrite=True)
+    ht.write(path_spark(htfile_rf_var_type_all_cols), overwrite=True)
 
 
 def main():
-    #set up
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
-    resourcedir = inputs['resource_dir']
+    # set up
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
+    resourcedir = config['general']['resource_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
-
-    truthset_file = resourcedir + "truthset_table.ht"
-    trio_stats_file = mtdir + "trio_stats.ht"
-    allele_data_file = mtdir + "allele_data.ht"
-    allele_counts_file = mtdir + "qc_ac.ht"
-    inbreeding_file = mtdir + "inbreeding.ht"
-
-   #mtfile = mtdir + "mt_pops_QC_filters_sequencing_location_and_superpop_sanger_only_after_sample_qc.mt"
-    mtfile = mtdir + "mt_varqc_splitmulti.mt"
-    htfile_rf_all_cols = mtdir + "ht_for_RF_all_cols.ht"
-    htfile_rf_var_type_all_cols = mtdir + "ht_for_RF_by_variant_type_all_cols.ht"
-
-    create_rf_ht(mtfile, truthset_file, trio_stats_file, allele_data_file, allele_counts_file, inbreeding_file, htfile_rf_all_cols, htfile_rf_var_type_all_cols)
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
+
+    truthset_file = config['step3']['create_rf_ht']['truthset_file']
+    trio_stats_file = config['step3']['create_rf_ht']['trio_stats_file']
+    allele_data_file = config['step3']['create_rf_ht']['allele_data_file']
+    allele_counts_file = config['step3']['create_rf_ht']['allele_counts_file']
+    inbreeding_file = config['step3']['create_rf_ht']['inbreeding_file']
+
+    # mtfile = mtdir + "mt_pops_QC_filters_sequencing_location_and_superpop_sanger_only_after_sample_qc.mt"
+    mtfile = config['step3']['create_rf_ht']['mtfile']
+    htoutfile_rf_all_cols = config['step3']['create_rf_ht']['htoutfile_rf_all_cols']
+    htoutfile_rf_var_type_all_cols = config['step3']['create_rf_ht']['htoutfile_rf_var_type_all_cols']
+
+    create_rf_ht(mtfile, truthset_file, trio_stats_file, 
+                 allele_data_file, allele_counts_file, 
+                 inbreeding_file, htoutfile_rf_all_cols, 
+                 htoutfile_rf_var_type_all_cols, config)
 
 
 if __name__ == '__main__':
diff --git a/3-variant_qc/3-train_rf.py b/3-variant_qc/3-train_rf.py
index 30e2db5..fa0b5c0 100755
--- a/3-variant_qc/3-train_rf.py
+++ b/3-variant_qc/3-train_rf.py
@@ -2,15 +2,29 @@
 import hail as hl
 import pyspark
 import uuid
+import argparse
 import json
 from pathlib import Path
 from typing import Dict, List, Tuple
 import utils.constants as constants
-from utils.utils import parse_config, get_rf
+from utils.utils import parse_config, get_rf, path_spark, path_local
 from gnomad.utils.file_utils import file_exists
 from gnomad.variant_qc.pipeline import train_rf_model
 from gnomad.variant_qc.random_forest import pretty_print_runs, save_model
 
+def get_options():
+    '''
+    Get options from the command line
+    '''
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument("--manual_runhash", 
+    help="Manually set the identifier of the RF run. Use for reproducible runs. Don't specify to generate a new run hash.", 
+    type=str)
+
+    args = parser.parse_args()
+    return args
+
 
 def get_rf_runs(rf_json_fp: str) -> Dict:
     """
@@ -28,13 +42,14 @@ def get_rf_runs(rf_json_fp: str) -> Dict:
         return {}
 
 
-def train_rf(ht: hl.Table, test_intervals: str) -> Tuple[hl.Table, pyspark.ml.PipelineModel]:
+def train_rf(ht: hl.Table, test_intervals: str, config: dict) -> Tuple[hl.Table, pyspark.ml.PipelineModel]:
     '''
     Train RF model
     :param hl.Table ht: Hail table containing input data
     :param str test_intervals: Test intervals
     :return: Hail table and RF model
     '''
+    conf = config['step3']['train_rf']
     features = constants.FEATURES
     print("test_intervals")
     print(test_intervals)
@@ -53,15 +68,16 @@ def train_rf(ht: hl.Table, test_intervals: str) -> Tuple[hl.Table, pyspark.ml.Pi
         print(hl.eval(test_intervals))
 
     ht=ht.persist()
-   
+    
+    # TODO: use kwargs expantions from the config as this is a gnomad package function
     rf_ht, rf_model = train_rf_model(
         ht,
         rf_features=features,
         tp_expr=ht.tp,
         fp_expr=ht.fp,
-        fp_to_tp=1.0,
-        num_trees=500,
-        max_depth=5,
+        fp_to_tp=conf['gnomad_train_rf_fp_to_tp'],
+        num_trees=conf['gnomad_train_rf_num_trees'],
+        max_depth=conf['gnomad_train_rf_max_depth'],
         test_expr=hl.literal(test_intervals).any(
             lambda interval: interval.contains(ht.locus)),
     )
@@ -124,31 +140,41 @@ def get_run_data(
 
 def main():
     # set up
-    inputs = parse_config()
-    rf_dir = inputs['var_qc_rf_dir']
-    mtdir = inputs['matrixtables_lustre_dir']
-    test_interval = inputs['rf_test_interval']
+    args = get_options()
+
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
+    rf_dir = path_spark(config['general']['var_qc_rf_dir'])
+
+    test_interval = config['step3']['rf_test_interval'] # used in multiple functions
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
+
+    # use manual hash value if provided to control the output folder name
+
+    # new hash is generated by default
+    run_hash = str(uuid.uuid4())[:8] # TODO: move to utils
+    rf_runs = get_rf_runs(path_spark(rf_dir))
+    if args.manual_runhash:
+        print(f'Using provided run ID: {args.manual_runhash}')
+        run_hash = args.manual_runhash
+    else:
+        # hash for new RF
+        while run_hash in rf_runs:
+            run_hash = str(uuid.uuid4())[:8]
 
-    # hash for new RF
-    run_hash = str(uuid.uuid4())[:8]
-    rf_runs = get_rf_runs(rf_dir)
-    while run_hash in rf_runs:
-        run_hash = str(uuid.uuid4())[:8]
-    
 
     # train RF
-    input_ht_file = mtdir + "ht_for_RF_by_variant_type_all_cols.ht"
-    input_ht = hl.read_table(input_ht_file)
-    runs_json = rf_dir + "rf_runs.json"
-    ht_result, rf_model = train_rf(input_ht, test_interval)
+    input_ht_file = config['step3']['train_rf']['input_ht_file']
+    input_ht = hl.read_table(path_spark(input_ht_file))
+    runs_json = config['step3']['runs_json']
+    ht_result, rf_model = train_rf(input_ht, test_interval, config)
     print("Writing out ht_training data")
-    ht_result = ht_result.checkpoint(get_rf(rf_dir, data="training", run_hash=run_hash).path, overwrite=True)
+    ht_result = ht_result.checkpoint(get_rf(path_spark(rf_dir), data="training", run_hash=run_hash).path, overwrite=True)
 
     rf_runs[run_hash] = get_run_data(
         vqsr_training=False,
@@ -160,11 +186,15 @@ def main():
     )
     rf_runs[run_hash]['features_importance'] = dict(rf_runs[run_hash]['features_importance'])#convert featues importance frozendict to dict for dumping to json
 
-    with hl.hadoop_open(runs_json, "w") as f:
+    print(f'Saving runs info in {runs_json}')
+    # TODO: not sure if this works as intended. Shouldn't the run info json file be saved in the corresponding run folder?
+    # If not, run info has to be appended, rather than overwriting existing runs.
+    #  
+    with hl.hadoop_open(path_spark(runs_json), "w") as f:
         json.dump(rf_runs, f)
     pretty_print_runs(rf_runs)
     save_model(
-            rf_model, get_rf(rf_dir, data="model", run_hash=run_hash), overwrite=True)
+            rf_model, get_rf(path_spark(rf_dir), data="model", run_hash=run_hash), overwrite=True)
 
 
 if __name__ == '__main__':
diff --git a/3-variant_qc/4-apply_rf.py b/3-variant_qc/4-apply_rf.py
index bac8912..8323e50 100755
--- a/3-variant_qc/4-apply_rf.py
+++ b/3-variant_qc/4-apply_rf.py
@@ -2,7 +2,7 @@
 import hail as hl
 import pyspark
 import argparse
-from utils.utils import parse_config, get_rf
+from utils.utils import parse_config, get_rf, path_spark, path_local
 import utils.constants as constants
 from gnomad.variant_qc.random_forest import apply_rf_model, load_model
 
@@ -24,22 +24,22 @@ def get_options():
 def main():
     # set up
     args = get_options()
-    inputs = parse_config()
-    rf_dir = inputs['var_qc_rf_dir']
+    config = parse_config()
+    rf_dir = path_spark(config['general']['var_qc_rf_dir']) # TODO: add adapters inside the functions to enhance robustness
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
     run_hash = args.runhash
-    rf_model = load_model(get_rf(rf_dir, data="model", run_hash=run_hash))
-    ht = get_rf(rf_dir, data="training", run_hash=run_hash).ht()
+    rf_model = load_model(get_rf(path_spark(rf_dir), data="model", run_hash=run_hash))
+    ht = get_rf(path_spark(rf_dir), data="training", run_hash=run_hash).ht()
     features = hl.eval(ht.features)
     ht = apply_rf_model(ht, rf_model, features, label=constants.LABEL_COL)
     ht = ht.annotate_globals(rf_hash=run_hash)
-    ht = ht.checkpoint(get_rf(rf_dir, "rf_result", run_hash=run_hash).path, overwrite=True)
+    ht = ht.checkpoint(get_rf(path_spark(rf_dir), "rf_result", run_hash=run_hash).path, overwrite=True)
     ht_summary = ht.group_by("tp", "fp", constants.TRAIN_COL, constants.LABEL_COL, constants.PREDICTION_COL).aggregate(n=hl.agg.count())
     ht_summary.show(n=20)
     
diff --git a/3-variant_qc/5-annotate_ht_after_rf.py b/3-variant_qc/5-annotate_ht_after_rf.py
index 41951f7..884e57c 100755
--- a/3-variant_qc/5-annotate_ht_after_rf.py
+++ b/3-variant_qc/5-annotate_ht_after_rf.py
@@ -2,7 +2,8 @@
 import hail as hl
 import pyspark
 import argparse
-from utils.utils import parse_config, rm_mt
+import os.path
+from utils.utils import parse_config, rm_mt, path_spark, path_local
 
 
 def get_options():
@@ -26,7 +27,10 @@ def add_cq_annotation(htfile: str, synonymous_file: str, ht_cq_file: str):
     ;param str synonymous_file: text file containing synonymous variants
     ;param str ht_cq_fle: Output hail table file annotated with synonymous variants
     '''
-    synonymous_ht=hl.import_table(synonymous_file,types={'f0':'str','f1':'int32', 'f2':'str','f3':'str','f4':'str', 'f5':'str'}, no_header=True)
+    # DEBUG: test if file:// prefix is needed for this function
+    synonymous_ht=hl.import_table(path_spark(synonymous_file), 
+                                  types={'f0': 'str', 'f1': 'int32', 'f2': 'str', 'f3': 'str', 'f4': 'str', 'f5': 'str'}, 
+                                  no_header=True)
     synonymous_ht=synonymous_ht.annotate(chr=synonymous_ht.f0)
     synonymous_ht=synonymous_ht.annotate(pos=synonymous_ht.f1)
     synonymous_ht=synonymous_ht.annotate(rs=synonymous_ht.f2)
@@ -39,9 +43,9 @@ def add_cq_annotation(htfile: str, synonymous_file: str, ht_cq_file: str):
     synonymous_ht=synonymous_ht.drop(synonymous_ht.f0,synonymous_ht.f1,synonymous_ht.f2,synonymous_ht.f3,synonymous_ht.f4,synonymous_ht.chr,synonymous_ht.pos,synonymous_ht.ref,synonymous_ht.alt)
     synonymous_ht = synonymous_ht.key_by(synonymous_ht.locus, synonymous_ht.alleles)
 
-    ht = hl.read_table(htfile)
+    ht = hl.read_table(path_spark(htfile))
     ht=ht.annotate(consequence=synonymous_ht[ht.key].consequence)
-    ht.write(ht_cq_file, overwrite=True)
+    ht.write(path_spark(ht_cq_file), overwrite=True)
 
 
 def dnm_and_family_annotation(ht_cq_fle: str, dnm_htfile: str, fam_stats_htfile: str, trio_stats_htfile: str, family_annot_htfile: str):
@@ -53,14 +57,14 @@ def dnm_and_family_annotation(ht_cq_fle: str, dnm_htfile: str, fam_stats_htfile:
     :param str trio_stats_htfile: Trio stats hail table file
     :param str family_annot_htfile: Output hail table annotated with DNMs and family stats file
     '''
-    ht = hl.read_table(ht_cq_fle)
-    dnm_ht = hl.read_table(dnm_htfile)
-    fam_stats_ht = hl.read_table(fam_stats_htfile)
-    trio_stats_ht = hl.read_table(trio_stats_htfile)
+    ht = hl.read_table(path_spark(ht_cq_fle))
+    dnm_ht = hl.read_table(path_spark(dnm_htfile))
+    fam_stats_ht = hl.read_table(path_spark(fam_stats_htfile))
+    trio_stats_ht = hl.read_table(path_spark(trio_stats_htfile))
     ht=ht.annotate(de_novo_data=dnm_ht[ht.key].de_novo_data)
     ht=ht.annotate(family_stats=fam_stats_ht[ht.key].family_stats)
     ht=ht.annotate(fam=trio_stats_ht[ht.key])
-    ht.write(family_annot_htfile, overwrite=True)
+    ht.write(path_spark(family_annot_htfile), overwrite=True)
 
 
 def count_trans_untransmitted_singletons(mt_filtered: hl.MatrixTable, ht: hl.Table) -> hl.Table:
@@ -88,7 +92,7 @@ def count_trans_untransmitted_singletons(mt_filtered: hl.MatrixTable, ht: hl.Tab
     
 
     
-    Total_transmitted_singletons=mt_trans_count.aggregate_entries(hl.agg.count_where(mt_trans_count.transmitted_singletons_count >0))
+    Total_transmitted_singletons=mt_trans_count.aggregate_entries(hl.agg.count_where(mt_trans_count.transmitted_singletons_count > 0))
     print(Total_transmitted_singletons)
     
     mt_untrans_count = (mt_untrans.group_cols_by(mt_untrans.id).aggregate(
@@ -101,7 +105,7 @@ def count_trans_untransmitted_singletons(mt_filtered: hl.MatrixTable, ht: hl.Tab
                     (mt_untrans.mother_entry.GT.is_non_ref())
                     )
                      )))
-    Total_untransmitted_singletons=mt_untrans_count.aggregate_entries(hl.agg.count_where(mt_untrans_count.untransmitted_singletons_count >0))
+    Total_untransmitted_singletons=mt_untrans_count.aggregate_entries(hl.agg.count_where(mt_untrans_count.untransmitted_singletons_count > 0))
     print(Total_untransmitted_singletons)
     
     print(f"\nTransmitted singletons:{Total_transmitted_singletons}\n")
@@ -118,7 +122,7 @@ def count_trans_untransmitted_singletons(mt_filtered: hl.MatrixTable, ht: hl.Tab
 
     ht=ht.annotate(variant_transmitted_singletons=mt2.rows()[ht.key].variant_transmitted_singletons)
     ht=ht.annotate(variant_untransmitted_singletons=mt3.rows()[ht.key].variant_untransmitted_singletons)
-    return(ht)    
+    return ht   
 
 
 def transmitted_singleton_annotation(family_annot_htfile: str, trio_mtfile: str, trio_filtered_mtfile: str, trans_sing_htfile: str):
@@ -130,18 +134,18 @@ def transmitted_singleton_annotation(family_annot_htfile: str, trio_mtfile: str,
     :param str trans_sing_htfile: Variant QC hail table file with transmitted singleton annotation
     '''
     print("Annotating with transmitted singletons")
-    ht = hl.read_table(family_annot_htfile)
-    mt_trios = hl.read_matrix_table(trio_mtfile)
+    ht = hl.read_table(path_spark(family_annot_htfile))
+    mt_trios = hl.read_matrix_table(path_spark(trio_mtfile))
     mt_trios = mt_trios.annotate_rows(consequence=ht[mt_trios.row_key].consequence)
     #there is a save step here in Pavlos file, is it needed? 
     # mt_filtered = mt_trios.filter_rows((mt_trios.variant_qc.AC[1] <= 2) & (mt_trios.consequence == "synonymous_variant"))
     # mt_filtered = mt_trios.filter_entries((mt_trios.variant_qc.AC[1] <= 2) & (mt_trios.consequence == "synonymous_variant"))
     mt_filtered = mt_trios.filter_rows((mt_trios.varqc_trios.AC[1] <= 2) & (mt_trios.consequence == "synonymous_variant"))
     mt_filtered = mt_trios.filter_entries((mt_trios.varqc_trios.AC[1] <= 2) & (mt_trios.consequence == "synonymous_variant"))
-    mt_filtered = mt_filtered.checkpoint(trio_filtered_mtfile, overwrite=True)
+    mt_filtered = mt_filtered.checkpoint(path_spark(trio_filtered_mtfile), overwrite=True)
 
     ht = count_trans_untransmitted_singletons(mt_filtered, ht)
-    ht.write(trans_sing_htfile, overwrite=True)
+    ht.write(path_spark(trans_sing_htfile), overwrite=True)
     rm_mt(trio_filtered_mtfile)
 
 
@@ -172,8 +176,8 @@ def annotate_gnomad(tdt_htfile: str, gnomad_htfile: str, final_htfile: str):
     :param str final_htfile: Final RF htfile for ranking and binning
     '''
     print("Annotating with gnomad AF")
-    ht = hl.read_table(tdt_htfile)
-    gnomad_ht = hl.read_table(gnomad_htfile)
+    ht = hl.read_table(path_spark(tdt_htfile))
+    gnomad_ht = hl.read_table(path_spark(gnomad_htfile))
     ht = ht.annotate(gnomad_af=gnomad_ht[ht.key].freq[0].AF)
     ht.write(final_htfile, overwrite = True)
 
@@ -181,33 +185,36 @@ def annotate_gnomad(tdt_htfile: str, gnomad_htfile: str, final_htfile: str):
 def main():
     # set up
     args = get_options()
-    inputs = parse_config()
-    rf_dir = inputs['var_qc_rf_dir']
-    mtdir = inputs['matrixtables_lustre_dir']
-    resourcedir = inputs['resource_dir']
+    config = parse_config()
+    rf_dir = path_spark(config['general']['var_qc_rf_dir']) # TODO: add adapters inside the functions to enhance robustness
+    mtdir = config['general']['matrixtables_dir']
+    resourcedir = config['general']['resource_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
-    htfile = rf_dir + args.runhash + "/rf_result.ht"
-    #annotate with synonymous CQs
-    synonymous_file = resourcedir + "synonymous_variants.txt"
-    ht_cq_file = rf_dir + args.runhash + "/rf_result_with_synonymous.ht"
+    # shouldn't be in the config as the run hash is provided through the command line
+    htfile = os.path.join(rf_dir, args.runhash, "rf_result.ht")
+
+    # annotate with synonymous CQs
+    synonymous_file = config['step3']['add_cq_annotation']['synonymous_file']
+    ht_cq_file = os.path.join(rf_dir, args.runhash, "rf_result_with_synonymous.ht")  # outfile
     add_cq_annotation(htfile, synonymous_file, ht_cq_file)
-    #annotate with family stats and DNMs
-    dnm_htfile = mtdir + "denovo_table.ht"
-    fam_stats_htfile = mtdir + "family_stats.ht"
-    trio_stats_htfile = mtdir + "trio_stats.ht"
-    family_annot_htfile = rf_dir + args.runhash + "/rf_result_denovo_family_stats.ht"
+
+    # annotate with family stats and DNMs
+    dnm_htfile = config['step3']['dnm_and_family_annotation']['dnm_htfile']
+    fam_stats_htfile = config['step3']['dnm_and_family_annotation']['fam_stats_htfile']
+    trio_stats_htfile = config['step3']['dnm_and_family_annotation']['trio_stats_htfile']
+    family_annot_htfile = os.path.join(rf_dir, args.runhash, "rf_result_denovo_family_stats.ht")  # outfile
     dnm_and_family_annotation(ht_cq_file, dnm_htfile, fam_stats_htfile, trio_stats_htfile, family_annot_htfile)
 
     #annotate with transmitted singletons
-    trio_mtfile = mtdir + "trios.mt"
-    trio_filtered_mtfile = mtdir + "trios_filtered_.mt"
-    trans_sing_htfile = rf_dir + args.runhash + "/rf_result_trans_sing.ht"
+    trio_mtfile = config['step3']['transmitted_singleton_annotation']['trio_mtfile']
+    trio_filtered_mtfile = config['step3']['transmitted_singleton_annotation']['trio_filtered_mtfile']
+    trans_sing_htfile = os.path.join(rf_dir, args.runhash, "rf_result_trans_sing.ht")  # outfile
     transmitted_singleton_annotation(family_annot_htfile, trio_mtfile, trio_filtered_mtfile, trans_sing_htfile)
 
     #annotate with number transmitted, number untransmitted (from transmission disequilibrium test)
@@ -217,8 +224,8 @@ def main():
     # run_tdt(mtfile, trans_sing_htfile, pedfile, tdt_htfile)
 
     #annotate with gnomad AF
-    final_htfile = rf_dir + args.runhash + "/rf_result_final_for_ranking.ht"
-    gnomad_htfile = resourcedir + "gnomad.exomes.r2.1.1.sites.liftover_grch38.ht"
+    final_htfile = os.path.join(rf_dir, args.runhash, "rf_result_final_for_ranking.ht")  # outfile
+    gnomad_htfile = config['step3']['annotate_gnomad']['gnomad_htfile']
     annotate_gnomad(trans_sing_htfile, gnomad_htfile, final_htfile)
 
 
diff --git a/3-variant_qc/6-rank_and_bin.py b/3-variant_qc/6-rank_and_bin.py
index b8b6db6..0475869 100755
--- a/3-variant_qc/6-rank_and_bin.py
+++ b/3-variant_qc/6-rank_and_bin.py
@@ -2,9 +2,10 @@
 import hail as hl
 import pyspark
 import argparse
+import os.path
 from typing import Optional, Dict
 from pprint import pformat
-from utils.utils import parse_config
+from utils.utils import parse_config, path_spark, path_local
 
 
 def get_options():
@@ -95,15 +96,17 @@ def add_rank(
     return ht
 
 
-def create_binned_data_initial(ht: hl.Table, bin_tmp_htfile: str, truth_htfile: str, n_bins: int) -> hl.Table:
+def create_binned_data_initial(ht: hl.Table, bin_tmp_htfile: str, truth_htfile: str, n_bins: int, config: dict) -> hl.Table:
     '''
     Create binned data from RF
     :param hl.Table ht: Input hail table
     :param str bin_tmp_htfile: Interim hail table file name
     :param str truth_htfile: Truth hail table file
     :param int n_bins: Number of bins to create
+    :param dict config: Dictionary with threshold values
     :return: Table with bins added
     '''
+    conf = config['step3']['create_binned_data_initial']
     # Count variants for ranking
     # count_expr = {x: hl.agg.filter(hl.is_defined(ht[x]), hl.agg.counter(hl.cond(hl.is_snp(
     #     ht.alleles[0], ht.alleles[1]), 'snv', 'indel'))) for x in ht.row if x.endswith('rank')}
@@ -112,7 +115,7 @@ def create_binned_data_initial(ht: hl.Table, bin_tmp_htfile: str, truth_htfile:
     rank_variant_counts = ht.aggregate(hl.Struct(**count_expr))
     print(f"Found the following variant counts:\n {pformat(rank_variant_counts)}")
 
-    ht_truth_data = hl.read_table(truth_htfile)
+    ht_truth_data = hl.read_table(path_spark(truth_htfile))
     ht = ht.annotate_globals(rank_variant_counts=rank_variant_counts)
     # ht = ht.annotate(
     #     **ht_truth_data[ht.key],
@@ -192,21 +195,21 @@ def create_binned_data_initial(ht: hl.Table, bin_tmp_htfile: str, truth_htfile:
             # n_clinvar=hl.agg.count_where(ht.clinvar),
             n_singleton=hl.agg.count_where(ht.transmitted_singleton),
             n_high_quality_de_novos=hl.agg.count_where(
-                ht.de_novo_data.p_de_novo[0] > 0.99),
+                ht.de_novo_data.p_de_novo[0] > conf['high_quality_p_de_novo']),
             #n_validated_DDD_denovos=hl.agg.count_where(
             #    ht.inheritance.contains("De novo")),
             n_medium_quality_de_novos=hl.agg.count_where(
-                ht.de_novo_data.p_de_novo[0] > 0.5),
+                ht.de_novo_data.p_de_novo[0] > conf['medium_quality_p_de_novo']),
             n_high_confidence_de_novos=hl.agg.count_where(
                 ht.de_novo_data.confidence[0] == 'HIGH'),
             n_de_novo=hl.agg.filter(ht.family_stats.unrelated_qc_callstats.AC[0][1] == 0, hl.agg.sum(
                 ht.family_stats.mendel[0].errors)),
             n_high_quality_de_novos_synonymous=hl.agg.count_where(
-                (ht.de_novo_data.p_de_novo[0] > 0.99) & (ht.consequence == "synonymous_variant")),
+                (ht.de_novo_data.p_de_novo[0] > conf['high_quality_p_de_novo']) & (ht.consequence == "synonymous_variant")),
             n_trans_singletons_synonymous_algorithm=hl.agg.count_where(
-                ht.variant_transmitted_singletons ==1 ),
+                ht.variant_transmitted_singletons == 1),
             n_untrans_singletons_synonymous_algorithm=hl.agg.count_where(
-                ht.variant_untransmitted_singletons ==1 ),
+                ht.variant_untransmitted_singletons == 1),
             # validated_de_novos=hl.agg.count_where(ht.validated_denovo_inheritance=="De novo constitutive"),
             # n_de_novo_no_lcr=hl.agg.filter(~ht.lcr & (
             #    ht.family_stats.unrelated_qc_callstats.AC[1] == 0), hl.agg.sum(ht.family_stats.mendel.errors)),
@@ -225,8 +228,8 @@ def create_binned_data_initial(ht: hl.Table, bin_tmp_htfile: str, truth_htfile:
             n_train_trans_singletons=hl.agg.count_where(
                 (ht.family_stats.unrelated_qc_callstats.AC[0][1] == 1) & (ht.family_stats.tdt[0].t == 1)),
             #transmitted and untransmitted common variants
-            n_trans_common=hl.agg.filter(ht.gnomad_af >= 0.1, hl.agg.sum(ht.family_stats.tdt[0].t)),
-            n_untrans_common=hl.agg.filter(ht.gnomad_af >= 0.1, hl.agg.sum(ht.family_stats.tdt[0].u)),
+            n_trans_common=hl.agg.filter(ht.gnomad_af >= conf['n_trans_common_gnomad_af'], hl.agg.sum(ht.family_stats.tdt[0].t)),
+            n_untrans_common=hl.agg.filter(ht.gnomad_af >= conf['n_untrans_common_gnomad_af'], hl.agg.sum(ht.family_stats.tdt[0].u)),
             #transmitted/untransmitted with Hail's TDT test
             n_trans_singletons_synonymous_tdt=hl.agg.count_where((ht.consequence == "synonymous_variant") & (
                 ht.family_stats.tdt[0].t == 1) & (ht.family_stats.tdt[0].u == 0)),
@@ -272,39 +275,40 @@ def create_binned_data_initial(ht: hl.Table, bin_tmp_htfile: str, truth_htfile:
 def main():
     # set up
     args = get_options()
-    inputs = parse_config()
-    rf_dir = inputs['var_qc_rf_dir']
-    resourcedir = inputs['resource_dir']
+    config = parse_config()
+    rf_dir = path_spark(config['general']['var_qc_rf_dir']) # TODO: add adapters inside the functions to enhance robustness
+    resourcedir = config['general']['resource_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
     # add rank
-    htfile = rf_dir + args.runhash + "/rf_result_final_for_ranking.ht"
-    htrankedfile = rf_dir + args.runhash + "/rf_result_ranked.ht"
-    ht = hl.read_table(htfile)
+    htfile = os.path.join(rf_dir, args.runhash, "rf_result_final_for_ranking.ht")
+    htrankedfile = os.path.join(rf_dir, args.runhash, "rf_result_ranked.ht")
+    ht = hl.read_table(path_spark(htfile))
     ht_ranked = add_rank(ht,
-                        score_expr=(1-ht.rf_probability["TP"]),
+                        score_expr=(1 - ht.rf_probability["TP"]),
                         subrank_expr={
                             'singleton_rank': ht.transmitted_singleton,
                             'biallelic_rank': ~ht.was_split,
                             'biallelic_singleton_rank': ~ht.was_split & ht.transmitted_singleton,
-                            'de_novo_high_quality_rank': ht.de_novo_data.p_de_novo[0] > 0.9,
-                            'de_novo_medium_quality_rank': ht.de_novo_data.p_de_novo[0] > 0.5,
+                            'de_novo_high_quality_rank': ht.de_novo_data.p_de_novo[0] > config['step3']['add_rank']['subrank_expr_de_novo_high_quality_rank'],
+                            'de_novo_medium_quality_rank': ht.de_novo_data.p_de_novo[0] > config['step3']['add_rank']['subrank_expr_de_novo_medium_quality_rank'],
                             'de_novo_synonymous_rank': ht.consequence == "synonymous_variant",
                         }
                         )
-    ht_ranked = ht_ranked.annotate(score=(1-ht_ranked.rf_probability["TP"]))
-    ht_ranked.write(htrankedfile, overwrite=True)
+    ht_ranked = ht_ranked.annotate(score=(1 - ht_ranked.rf_probability["TP"]))
+    ht_ranked.write(path_spark(htrankedfile), overwrite=True)
     # add bins
-    truth_htfile = resourcedir + "truthset_table.ht"
-    bin_tmp_htfile = rf_dir + args.runhash + "/_gnomad_score_binning_tmp.ht"
-    ht_bins = create_binned_data_initial(ht_ranked, bin_tmp_htfile, truth_htfile, n_bins=100)
-    bin_htfile = rf_dir + args.runhash + "/_rf_result_ranked_BINS.ht"
-    ht_bins.write(bin_htfile, overwrite=True)
+    truth_htfile = config['step3']['create_binned_data_initial']['truth_htfile']
+    bin_tmp_htfile = os.path.join(rf_dir, args.runhash, "_gnomad_score_binning_tmp.ht")
+    ht_bins = create_binned_data_initial(ht_ranked, bin_tmp_htfile, truth_htfile, n_bins=100, config=config)
+
+    bin_htfile = os.path.join(rf_dir, args.runhash, "_rf_result_ranked_BINS.ht")
+    ht_bins.write(path_spark(bin_htfile), overwrite=True)
 
 
 if __name__ == '__main__':
diff --git a/3-variant_qc/7-plot_rf_output.py b/3-variant_qc/7-plot_rf_output.py
index 1494dce..af8da68 100755
--- a/3-variant_qc/7-plot_rf_output.py
+++ b/3-variant_qc/7-plot_rf_output.py
@@ -4,12 +4,14 @@
 import os
 import argparse
 import pandas as pd
-from typing import Union, Dict, List, Set, Tuple
-from bokeh.models import Plot, Row, Span
-from bokeh.plotting import output_file, save
+import numpy as np
+from typing import Union, Dict, List, Set, Tuple, Callable
+import bokeh.models as bm
+from bokeh.models.layouts import TabPanel
+from bokeh.plotting import output_file, save, figure
 from gnomad.utils.plotting import *
 from hail.plot import show, output_notebook
-from utils.utils import parse_config
+from utils.utils import parse_config, path_spark, path_local
 
 
 def get_options():
@@ -26,12 +28,13 @@ def get_options():
     return args
 
 
-def set_plots_defaults(p: Plot, qc_plots_settings: dict) -> None:
+# TODO: move to utils?
+def set_plots_defaults(p: bm.Plot, qc_plots_settings: dict) -> None:
     p.legend.label_text_font_size = qc_plots_settings['label_text_font_size']
-    p.title.text_font_size = qc_plots_settings['title.text_font_size']
-    p.axis.axis_label_text_font_size = qc_plots_settings['axis.axis_label_text_font_size']
-    p.axis.axis_label_text_font_style = qc_plots_settings['axis.axis_label_text_font_style']
-    p.axis.major_label_text_font_size = qc_plots_settings['axis.major_label_text_font_size']
+    p.title.text_font_size = qc_plots_settings['title_text_font_size']
+    p.axis.axis_label_text_font_size = qc_plots_settings['axis_axis_label_text_font_size']
+    p.axis.axis_label_text_font_style = qc_plots_settings['axis_axis_label_text_font_style']
+    p.axis.major_label_text_font_size = qc_plots_settings['axis_major_label_text_font_size']
 
     
 def get_point_size_col(data: pd.Series, size_prop: str, qc_plots_settings: dict) -> pd.Series:
@@ -74,7 +77,7 @@ def plot_metric(df: pd.DataFrame,
                 colors: Dict[str, str] = None,
                 link_cumul_y: bool = True,
                 size_prop: str = 'area'
-                ) -> Tabs:
+                ) -> bm.Tabs:
     """
     Generic function for generating QC metric plots using a plotting-ready DataFrame (obtained from `get_binned_models_pd`)
     DataFrame needs to have a `rank_id` column, a `bin` column and a `model` column (contains the model name and needs to be added to binned table(s))
@@ -106,10 +109,10 @@ def plot_metric(df: pd.DataFrame,
     :param dict of str -> str colors: Mapping of model name -> color
     :param bool link_cumul_y: If set, y-axes of cumulative and non-cumulative plots are linked
     :param str size_prop: Either 'size' or 'area' can be specified. If either is specified, the points will be sized proportionally to the amount of data in that point.
-    :return: Plot
-    :rtype: Tabs
+    :return: bm.Plot
+    :rtype: bm.Tabs
     """
-    def get_row(df: pd.DataFrame, y_name: str, cols: List[str], y_fun: Callable[[pd.Series], Union[float, int]], titles: List[str], link_cumul_y: bool, cut: int = None) -> Row:
+    def get_row(df: pd.DataFrame, y_name: str, cols: List[str], y_fun: Callable[[pd.Series], Union[float, int]], titles: List[str], link_cumul_y: bool, cut: int = None) -> bm.Row:
         """
         Generates a single row with two plots: a regular scatter plot and a cumulative one.
         Both plots have bins on the x-axis. The y-axis is computed by applying the function `y_fun` on the columns `cols`.
@@ -120,7 +123,7 @@ def get_row(df: pd.DataFrame, y_name: str, cols: List[str], y_fun: Callable[[pd.
 
         """
 
-        def get_plot(data_source: ColumnDataSource, y_name: str, y_col_name: str, titles: List[str], data_ranges: Tuple[DataRange1d, DataRange1d], cut: int = None) -> Plot:
+        def get_plot(data_source: bm.ColumnDataSource, y_name: str, y_col_name: str, titles: List[str], data_ranges: Tuple[bm.DataRange1d, bm.DataRange1d], cut: int = None) -> bm.Plot:
             """
             Generates a single scatter plot panel
             """
@@ -134,16 +137,16 @@ def get_plot(data_source: ColumnDataSource, y_name: str, y_col_name: str, titles
             p.y_range = data_ranges[1]
 
             if cut:
-                p.add_layout(Span(location=cut, dimension='height', line_color='red', line_dash='dashed'))
+                p.add_layout(bm.Row(location=cut, dimension='height', line_color='red', line_dash='dashed'))
 
             # Add circles layouts one model at a time, so that no default legend is generated.
-            # Because data is in the same ColumnDataSource, use a BooleanFilter to plot each model separately
+            # Because data is in the same bm.ColumnDataSource, use a bm.BooleanFilter to plot each model separately
             circles = []
             for model in set(data_source.data['model']):
-                view = CDSView(source=data_source, filters=[BooleanFilter([x == model for x in data_source.data['model']])])
+                view = bm.CDSView(source=data_source, filters=[bm.BooleanFilter([x == model for x in data_source.data['model']])])
                 circles.append((model, [p.circle('bin', y_col_name, color='_color', size='_size', source=data_source, view=view)]))
 
-            p.select_one(HoverTool).tooltips = [('model', '@model'),
+            p.select_one(bm.HoverTool).tooltips = [('model', '@model'),
                                                 ('bin', '@bin'),
                                                 (y_name, f'@{y_col_name}'),
                                                 ('min_score', '@min_score'),
@@ -153,12 +156,12 @@ def get_plot(data_source: ColumnDataSource, y_name: str, y_col_name: str, titles
             set_plots_defaults(p, qc_plots_settings)
 
             # Add legend above the plot area
-            legend = Legend(items=circles, orientation='horizontal', location=(0, 0), click_policy="hide")
+            legend = bm.Legend(items=circles, orientation='horizontal', location=(0, 0), click_policy="hide")
             p.add_layout(legend, 'above')
 
             # Add subtitles if any
             for title in titles[1:]:
-                p.add_layout(Title(text=title, text_font_size=qc_plots_settings['subtitle.text_font_size']), 'above')
+                p.add_layout(bm.Title(text=title, text_font_size=qc_plots_settings['subtitle_text_font_size']), 'above')
 
             return p
         # Compute non-cumulative values by applying `y_fun`
@@ -166,15 +169,15 @@ def get_plot(data_source: ColumnDataSource, y_name: str, y_col_name: str, titles
 
         # Compute cumulative values for each of the data columns
         for col in cols:
-            df[f'{col}_cumul'] = df.groupby('model').aggregate(np.cumsum)[col]
+            df[f'{col}_cumul'] = df.groupby('model')[col].aggregate(np.cumsum)
         df['cumul'] = df[[f'{col}_cumul' for col in cols]].apply(y_fun, axis=1)
 
         # Create data ranges that are either shared or distinct depending on the y_cumul parameter
-        non_cumul_data_ranges = (DataRange1d(), DataRange1d())
-        cumul_data_ranges = non_cumul_data_ranges if link_cumul_y else (non_cumul_data_ranges[0], DataRange1d())
-        data_source = ColumnDataSource(df)
+        non_cumul_data_ranges = (bm.DataRange1d(), bm.DataRange1d())
+        cumul_data_ranges = non_cumul_data_ranges if link_cumul_y else (non_cumul_data_ranges[0], bm.DataRange1d())
+        data_source = bm.ColumnDataSource(df)
 
-        return Row(get_plot(data_source, y_name, 'non_cumul', titles, non_cumul_data_ranges, cut),
+        return bm.Row(get_plot(data_source, y_name, 'non_cumul', titles, non_cumul_data_ranges, cut),
                    get_plot(data_source, y_name, 'cumul', [titles[0] + ', cumulative'] + titles[1:], cumul_data_ranges, cut))
 
     
@@ -209,7 +212,7 @@ def prepare_pd(df: pd.DataFrame, cols: List[str], colors: Dict[str, str] = {}, s
                 print('No data found for plot: {}'.format('\t'.join(titles)))
 
         if children:
-            tabs.append(Panel(child=Column(children=children), title='All'))
+            tabs.append(TabPanel(child=bm.Column(children=children), title='All'))
 
    
     if plot_singletons:
@@ -224,9 +227,9 @@ def prepare_pd(df: pd.DataFrame, cols: List[str], colors: Dict[str, str] = {}, s
                     print('No data found for plot: {}'.format('\t'.join(titles)))
 
         if children:
-            tabs.append(Panel(child=Column(children=children), title='Singletons'))
+            tabs.append(TabPanel(child=bm.Column(children=children), title='Singletons'))
 
-    return Tabs(tabs=tabs)
+    return bm.Tabs(tabs=tabs)
 
 
 def create_plots(bin_htfile: str, plot_dir: str, run_hash: str, qc_plots_settings: dict):
@@ -259,83 +262,83 @@ def create_plots(bin_htfile: str, plot_dir: str, run_hash: str, qc_plots_setting
     model = run_hash
     colors = {model:'blue'}
     #plot transmitted singletons
-    plotfile = plot_dir + "transmitted_singletons.html"
+    plotfile = os.path.join(plot_dir, "transmitted_singletons.html")
     tabs = plot_metric(snvs, 'n_trans_singletons', ['n_trans_singletons_synonymous_algorithm'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot untransmitted singletons
-    plotfile = plot_dir + "untransmitted_singletons.html"
+    plotfile = os.path.join(plot_dir, "untransmitted_singletons.html")
     tabs = plot_metric(snvs, 'n_untrans_singletons', ['n_untrans_singletons_synonymous_algorithm'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot transmitted/untransmitted ratio
-    plotfile = plot_dir + "transmitted_untransmitted.html"
+    plotfile = os.path.join(plot_dir, "transmitted_untransmitted.html")
     tabs = plot_metric(snvs, 'trans_untrans_ratio', ['n_trans_singletons_synonymous_algorithm', 'n_untrans_singletons_synonymous_algorithm'], qc_plots_settings, y_fun=lambda x: x[0]/x[1], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot number of insertions
-    plotfile = plot_dir + "n_insertions.html"
+    plotfile = os.path.join(plot_dir, "n_insertions.html")
     tabs = plot_metric(indels, 'n_ins', ['n_ins'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot number of deletions
-    plotfile = plot_dir + "n_deletions.html"
+    plotfile = os.path.join(plot_dir, "n_deletions.html")
     tabs = plot_metric(indels, 'n_del', ['n_del'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot Ti/Tv ratio
-    plotfile = plot_dir + "r_ti_tv.html"
+    plotfile = os.path.join(plot_dir, "r_ti_tv.html")
     tabs = plot_metric(snvs, 'Ti/Tv ratio', ['n_ti', 'n_tv'], qc_plots_settings, y_fun=lambda x: x[0]/x[1], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot 1kg high confidence SNVs
-    plotfile = plot_dir + "kg_snv.html"
+    plotfile = os.path.join(plot_dir, "kg_snv.html")
     tabs = plot_metric(snvs, 'n_kgp_high_conf_snvs', ['n_kgp_high_conf_snvs'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot omni SNVs
-    plotfile = plot_dir + "omni_snv.html"
+    plotfile = os.path.join(plot_dir, "omni_snv.html")
     tabs = plot_metric(snvs, 'n_omni', ['n_omni'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot mills indels
-    plotfile = plot_dir + "mills_indels.html"
+    plotfile = os.path.join(plot_dir, "mills_indels.html")
     tabs = plot_metric(indels, 'n_mills', ['n_mills'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot hapmap snvs
-    plotfile = plot_dir + "hapmap_snvs.html"
+    plotfile = os.path.join(plot_dir, "hapmap_snvs.html")
     tabs = plot_metric(snvs, 'n_hapmap_snvs', ['n_hapmap'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot hapmap indels
-    plotfile = plot_dir + "hapmap_indels.html"
+    plotfile = os.path.join(plot_dir, "hapmap_indels.html")
     tabs = plot_metric(indels, 'n_hapmap_indels', ['n_hapmap'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot fail hard filters snvs
-    plotfile = plot_dir + "fail_hard_filters_snvs.html"
+    plotfile = os.path.join(plot_dir, "fail_hard_filters_snvs.html")
     tabs = plot_metric(snvs, 'fail_hard_filters_snvs', ['fail_hard_filters_snvs'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot fail hard filters indels
-    plotfile = plot_dir + "fail_hard_filters_indels.html"
+    plotfile = os.path.join(plot_dir, "fail_hard_filters_indels.html")
     tabs = plot_metric(indels, 'fail_hard_filters_indels', ['fail_hard_filters_indels'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot transmitted/untransmitted from Hail's tdt test
     #plot transmitted singletons
-    plotfile = plot_dir + "transmitted_singletons_tdt.html"
+    plotfile = os.path.join(plot_dir, "transmitted_singletons_tdt.html")
     tabs = plot_metric(snvs, 'n_trans_singletons_tdt', ['n_trans_singletons_synonymous_tdt'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #plot untransmitted singletons
-    plotfile = plot_dir + "untransmitted_singletons_tdt.html"
+    plotfile = os.path.join(plot_dir, "untransmitted_singletons_tdt.html")
     tabs = plot_metric(snvs, 'n_untrans_singletons_tdt', ['n_untrans_singletons_synonymous_tdt'], qc_plots_settings, y_fun=lambda x: x[0], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
     #ratio
-    plotfile = plot_dir + "transmitted_untransmitted_tdt.html"
+    plotfile = os.path.join(plot_dir, "transmitted_untransmitted_tdt.html")
     tabs = plot_metric(snvs, 'trans_untrans_ratio_tdt', ['n_trans_singletons_synonymous_tdt', 'n_untrans_singletons_synonymous_tdt'], qc_plots_settings, y_fun=lambda x: x[0]/x[1], plot_bi_allelics=False, plot_singletons=False, plot_bi_allelic_singletons=False, colors=colors)
     output_file(filename=plotfile)
     save(tabs)
@@ -374,26 +377,30 @@ def create_plots(bin_htfile: str, plot_dir: str, run_hash: str, qc_plots_setting
 def main():
     # set up
     args = get_options()
-    inputs = parse_config()
-    rf_dir = inputs['var_qc_rf_dir']
-    root_plot_dir = inputs['plots_dir_local']
-
-    qc_plots_settings = {
-        'mean_point_size': 4.0,
-        'min_point_size': 1.0,
-        'max_point_size': 16.0,
-        'label_text_font_size': "14pt",
-        'title.text_font_size': "16pt",
-        'subtitle.text_font_size': "14pt",
-        'axis.axis_label_text_font_size': "16pt",
-        'axis.axis_label_text_font_style': "normal",
-        'axis.major_label_text_font_size': "14pt"
-    }
-    plot_dir = root_plot_dir + "variant_qc/" + args.runhash + "/"
-    if not os.path.exists(plot_dir):
-        os.makedirs(plot_dir)
-
-    bin_htfile = rf_dir + args.runhash + "/_rf_result_ranked_BINS.ht"
+    config = parse_config()
+    rf_dir = path_spark(config['general']['var_qc_rf_dir']) # TODO: add adapters inside the functions to enhance robustness
+    root_plot_dir = config['general']['plots_dir']
+
+    # TODO DEBUG: test if this way works
+    qc_plots_settings = config['step3']['create_plots']['qc_plots_settings']
+
+    ## TODO DEBUG: otherwise specify individual parameters manually
+    # qc_plots_settings = {
+    #     'mean_point_size': 4.0,
+    #     'min_point_size': 1.0,
+    #     'max_point_size': 16.0,
+    #     'label_text_font_size': "14pt",
+    #     'title.text_font_size': "16pt",
+    #     'subtitle.text_font_size': "14pt",
+    #     'axis.axis_label_text_font_size': "16pt",
+    #     'axis.axis_label_text_font_style': "normal",
+    #     'axis.major_label_text_font_size': "14pt"
+    # }
+
+    plot_dir = os.path.join(root_plot_dir, "variant_qc", args.runhash)
+    os.makedirs(plot_dir, exist_ok=True)  # create if doesn't exist
+
+    bin_htfile = os.path.join(rf_dir, args.runhash, "_rf_result_ranked_BINS.ht")
     create_plots(bin_htfile, plot_dir, args.runhash, qc_plots_settings)
 
 
diff --git a/3-variant_qc/8-select_thresholds.py b/3-variant_qc/8-select_thresholds.py
index 5c33437..dc408ee 100755
--- a/3-variant_qc/8-select_thresholds.py
+++ b/3-variant_qc/8-select_thresholds.py
@@ -3,7 +3,8 @@
 import hail as hl
 import pyspark
 import argparse
-from utils.utils import parse_config
+import os.path
+from utils.utils import parse_config, path_spark, path_local
 
 
 def get_options():
@@ -11,7 +12,7 @@ def get_options():
     Get options from the command line
     '''
     parser = argparse.ArgumentParser()
-    parser.add_argument("--runhash", help="RF run hash")
+    parser.add_argument("--runhash", help = "RF run hash") # TODO: move to config?
     parser.add_argument("--snv", help = "Proposed SNV threshold")
     parser.add_argument("--indel", help = "Proposed Indel threshold")
     args = parser.parse_args()
@@ -35,7 +36,7 @@ def analyse_thresholds(htfile: str, snv_threshold: int, indel_threshold: int):
     snv_t = get_threshold_range(snv_threshold)
     indel_t = get_threshold_range(indel_threshold)
     
-    ht = hl.read_table(htfile)
+    ht = hl.read_table(path_spark(htfile))
     #keep only those with rank_id = rank
     ht = ht.filter(ht.rank_id == 'rank')
     #split by snv and indel
@@ -52,21 +53,21 @@ def analyse_thresholds(htfile: str, snv_threshold: int, indel_threshold: int):
     print_results(indel_result)
 
 
+# TODO: move to utils?
 def print_results(result: dict):
     '''
     Print percentages of variants kept at each threshold
     :param dict result: Results to print
     '''
     for t in result.keys():
-        print("bin " + str(t) + ": " + '{0:.3f}'.format(result[t]['tp_pc']) + " percent TPs remain, "
-         + '{0:.3f}'.format(result[t]['fp_pc']) + " percent FPs remain" )
+        print(f"bin {str(t)}: {result[t]['tp_pc']:.3f} percent TPs remain, {result[t]['fp_pc']:.3f} percent FPs remain")
 
-
-def get_vars_kept(ht: hl.Table, t_list: list):
+def get_vars_kept(ht: hl.Table, t_list: list) -> dict:
     '''
     find proportions fo TP and FPs kept in ht for each threshold in t_list
     :param hl.Table ht: input Hail Table
     :param list t_list: List of thresholds
+    :return: Dictionary with TP and FP proportions for the gived thresholds
     '''
     results = {}
     ht_TP = ht.filter(ht.tp == True)
@@ -77,28 +78,30 @@ def get_vars_kept(ht: hl.Table, t_list: list):
         results[t] = {}
         ht_tp_pass = ht_TP.filter(ht_TP.bin <= t)
         tp_pass = ht_tp_pass.count()
-        results[t]['tp_pc'] = 100*(tp_pass/tp_total)
+        results[t]['tp_pc'] = 100 * (tp_pass / tp_total)
         ht_fp_pass = ht_FP.filter(ht_FP.bin <= t)
         fp_pass = ht_fp_pass.count()
-        results[t]['fp_pc'] = 100*(fp_pass/fp_total)
+        results[t]['fp_pc'] = 100 * (fp_pass / fp_total)
 
     return results
     
 
+# TODO: should this be configurable through config? 
 def get_threshold_range(threshold: int):
     '''
     Given a single threshold value convert to a range - for each threshold also look at 3 bins on either 
     side and +/-5 (unless <1 or >101)
     :param int threshold: single threshold value
+    :return: list of thresholds
     '''
-    t_list = list(range(threshold-3, threshold+4))
-    min_t = t_list[0]-5
-    max_t = t_list[6]+5
-    t_list.insert(0,min_t)
+    t_list = list(range(threshold - 3, threshold + 4))
+    min_t = t_list[0] - 5
+    max_t = t_list[6] + 5
+    t_list.insert(0, min_t)
     t_list.append(max_t)
-    while t_list[len(t_list)-1] > 101:
+    while t_list[len(t_list) - 1] > 101:
         t_list.pop()
-    while(t_list[0] < 1):
+    while t_list[0] < 1:
         t_list.pop[0]
 
     return t_list
@@ -107,16 +110,16 @@ def get_threshold_range(threshold: int):
 def main():
     # set up
     args = get_options()
-    inputs = parse_config()
-    rf_dir = inputs['var_qc_rf_dir']
+    config = parse_config()
+    rf_dir = path_spark(config['general']['var_qc_rf_dir']) # TODO: add adapters inside the functions to enhance robustness
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
-    htfile = rf_dir + args.runhash + "/_gnomad_score_binning_tmp.ht"
+    htfile = os.path.join(rf_dir, args.runhash, "_gnomad_score_binning_tmp.ht")
     analyse_thresholds(htfile, args.snv, args.indel)
 
 
diff --git a/3-variant_qc/9-filter_mt_after_variant_qc.py b/3-variant_qc/9-filter_mt_after_variant_qc.py
index 2cfcede..fa8bcab 100755
--- a/3-variant_qc/9-filter_mt_after_variant_qc.py
+++ b/3-variant_qc/9-filter_mt_after_variant_qc.py
@@ -2,7 +2,8 @@
 import hail as hl
 import pyspark
 import argparse
-from utils.utils import parse_config
+import os.path
+from utils.utils import parse_config, path_spark, path_local
 
 
 def get_options():
@@ -31,8 +32,8 @@ def annotate_mt_with_cq_rf_score_and_bin(mtfile: str, rf_htfile: str, snv_thresh
     :param str cqfile: File containing consequence annotation
     :param str filtered_mtfile: random forest score annotated mtfile
     '''
-    mt = hl.read_matrix_table(mtfile)
-    rf_ht = hl.read_table(rf_htfile)
+    mt = hl.read_matrix_table(path_spark(mtfile))
+    rf_ht = hl.read_table(path_spark(rf_htfile))
 
     # keep only vars with rank_id = rank
     rf_ht = rf_ht.filter(rf_ht.rank_id == 'rank')
@@ -48,8 +49,10 @@ def annotate_mt_with_cq_rf_score_and_bin(mtfile: str, rf_htfile: str, snv_thresh
     )
 
     # annotate with VEP consequence
-    cq_ht = hl.import_table(cqfile, types={'f0': 'str', 'f1': 'int32', 'f2': 'str',
-                            'f3': 'str', 'f4': 'str', 'f5': 'str'}, no_header=True)
+    cq_ht = hl.import_table(path_spark(cqfile), 
+                            types={'f0': 'str', 'f1': 'int32', 'f2': 'str',
+                            'f3': 'str', 'f4': 'str', 'f5': 'str'}, 
+                            no_header=True)
     cq_ht = cq_ht.annotate(chr=cq_ht.f0)
     cq_ht = cq_ht.annotate(pos=cq_ht.f1)
     cq_ht = cq_ht.annotate(rs=cq_ht.f2)
@@ -69,33 +72,34 @@ def annotate_mt_with_cq_rf_score_and_bin(mtfile: str, rf_htfile: str, snv_thresh
     mt_filtered = mt.filter_rows(((hl.is_snp(mt.alleles[0], mt.alleles[1])) & (mt.info.rf_bin <= snv_threshold)) | (
         (hl.is_indel(mt.alleles[0], mt.alleles[1])) & (mt.info.rf_bin <= indel_threshold)))
 
-    mt_filtered.write(filtered_mtfile, overwrite = True)
+    mt_filtered.write(path_spark(filtered_mtfile), overwrite = True)
 
     nvars = mt.count_rows()
     nvar_filtered = mt_filtered.count_rows()
-    print(str(nvars) + " variants before filtering, " + str(nvar_filtered) + " variants after filtering")
+    print(f'{str(nvars)} variants before filtering, {str(nvar_filtered)} variants after filtering')
 
 
 def main():
     # set up
     args = get_options()
-    inputs = parse_config()
-    rf_dir = inputs['var_qc_rf_dir']
-    mtdir = inputs['matrixtables_lustre_dir']
-    resourcedir = inputs['resource_dir']
+    config = parse_config()
+    rf_dir = path_spark(config['general']['var_qc_rf_dir']) # TODO: add adapters inside the functions to enhance robustness
+    mtdir = config['general']['matrixtables_dir']
+    resourcedir = config['general']['resource_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
-    htfile = rf_dir + args.runhash + "/_gnomad_score_binning_tmp.ht"
-    mtfile = mtdir + "mt_varqc_splitmulti.mt"
-    mtfile_after_varqc = mtdir + "mt_after_var_qc.mt"
-    cqfile = resourcedir + "all_consequences.txt"
+    htfile = os.path.join(rf_dir, args.runhash, "_gnomad_score_binning_tmp.ht")
 
-    annotate_mt_with_cq_rf_score_and_bin(mtfile, htfile, args.snv, args.indel, cqfile, mtfile_after_varqc)
+    mtfile = config['step3']['annotate_mt_with_cq_rf_score_and_bin']['mtfile']
+    cqfile = config['step3']['annotate_mt_with_cq_rf_score_and_bin']['cqfile']
+    mtoutfile_after_varqc = config['step3']['annotate_mt_with_cq_rf_score_and_bin']['mtoutfile_after_varqc']
+
+    annotate_mt_with_cq_rf_score_and_bin(mtfile, htfile, args.snv, args.indel, cqfile, mtoutfile_after_varqc)
 
 
 if __name__ == '__main__':
diff --git a/3-variant_qc/variant_qc_non_trios/1-generate_truth_sets_non_trios.py b/3-variant_qc/variant_qc_non_trios/1-generate_truth_sets_non_trios.py
index 0a08cdf..bec70e4 100644
--- a/3-variant_qc/variant_qc_non_trios/1-generate_truth_sets_non_trios.py
+++ b/3-variant_qc/variant_qc_non_trios/1-generate_truth_sets_non_trios.py
@@ -3,7 +3,7 @@
 import pyspark
 import argparse
 from typing import Tuple
-from wes_qc.utils.utils import parse_config
+from utils.utils import parse_config, path_spark, path_local
 from gnomad.utils.filtering import filter_to_adj, filter_to_autosomes
 from gnomad.utils.annotations import unphase_call_expr, bi_allelic_site_inbreeding_expr, add_variant_type, annotate_adj, bi_allelic_expr
 from gnomad.sample_qc.relatedness import generate_trio_stats_expr
@@ -28,7 +28,7 @@ def get_options():
     return args
 
 
-def get_truth_ht(omni, mills, thousand_genomes, hapmap, truth_ht_file):
+def get_truth_ht(omni: str, mills: str, thousand_genomes: str, hapmap: str, truth_ht_file: str) -> None:
     '''
     Generate truth set HT
     :param str omni: file containing kgp_omni 1000 Genomes intersection Onni 2.5M array
@@ -37,19 +37,19 @@ def get_truth_ht(omni, mills, thousand_genomes, hapmap, truth_ht_file):
     :param str hapmap: file containing hapmap
     :param str truth_ht_file: output file name
     '''
-    omni_ht = hl.read_table(omni)
-    mills_ht = hl.read_table(mills)
-    thousand_genomes_ht = hl.read_table(thousand_genomes)
-    hapmap_ht = hl.read_table(hapmap)
+    omni_ht = hl.read_table(path_spark(omni))
+    mills_ht = hl.read_table(path_spark(mills))
+    thousand_genomes_ht = hl.read_table(path_spark(thousand_genomes))
+    hapmap_ht = hl.read_table(path_spark(hapmap))
 
     truth_ht = hapmap_ht.select(hapmap=True).join(
         omni_ht.select(omni=True), how="outer").join(
             thousand_genomes_ht.select(kgp_phase1_hc=True), how="outer").join(
                 mills_ht.select(mills=True), how="outer").repartition(200, shuffle=False)
-    truth_ht.write(truth_ht_file, overwrite=True)
+    truth_ht.write(path_spark(truth_ht_file), overwrite=True)
     
 
-def split_multi_and_var_qc(mtfile: str, varqc_mtfile: str, varqc_mtfile_split: str):
+def split_multi_and_var_qc(mtfile: str, varqc_mtfile: str, varqc_mtfile_split: str) -> None:
     '''
     Adapted from https://github.com/broadinstitute/gnomad_qc/blob/3d79bdf0f7049c209b4659ff8c418a1b859d7cfa/gnomad_qc/v2/annotations/generate_qc_annotations.py
     Run split_multi_hts and variant QC on inout mt after sample QC
@@ -57,17 +57,17 @@ def split_multi_and_var_qc(mtfile: str, varqc_mtfile: str, varqc_mtfile_split: s
     :param str varqc_mtfile: Output mt with variant QC annotation 
     :param str varqc_mtfile_split: Output mt with variant QC annotation and split multiallelics
     '''
-    mt = hl.read_matrix_table(mtfile)
+    mt = hl.read_matrix_table(path_spark(mtfile))
 
     #before splitting annotate with sum_ad
     mt = mt.annotate_entries(sum_AD = hl.sum(mt.AD))
     mt = annotate_adj(mt)
-    mt.write(varqc_mtfile, overwrite=True)
+    mt.write(path_spark(varqc_mtfile), overwrite=True)
     mt = hl.split_multi_hts(mt)
     
     tmp_mt = varqc_mtfile_split + "_tmp"
     print("writing split mt")
-    mt.write(tmp_mt, overwrite=True)
+    mt.write(path_spark(tmp_mt), overwrite=True)
 
     mt = hl.variant_qc(mt)
     mt = mt.filter_rows(mt.variant_qc.n_non_ref == 0, keep = False)
@@ -88,7 +88,7 @@ def split_multi_and_var_qc(mtfile: str, varqc_mtfile: str, varqc_mtfile_split: s
     )
 
     print("writing split mt")
-    mt.write(varqc_mtfile_split, overwrite=True)
+    mt.write(path_spark(varqc_mtfile_split), overwrite=True)
 
 
 def read_fam(fam_file: str) -> hl.Table:
@@ -96,14 +96,14 @@ def read_fam(fam_file: str) -> hl.Table:
     Taken from https://github.com/broadinstitute/gnomad_qc/blob/3d79bdf0f7049c209b4659ff8c418a1b859d7cfa/gnomad_qc/v2/annotations/generate_qc_annotations.py
     '''
     columns = ['fam_id', 's', 'pat_id', 'mat_id', 'is_female']
-    return hl.import_table(fam_file, no_header=True).rename({f'f{i}': c for i, c in enumerate(columns)}).key_by('s')
+    return hl.import_table(path_spark(fam_file), no_header=True).rename({f'f{i}': c for i, c in enumerate(columns)}).key_by('s')
 
 
 def annotate_unrelated_sample(mt: hl.MatrixTable, fam_file: str) -> hl.MatrixTable:
     '''
     Taken from https://github.com/broadinstitute/gnomad_qc/blob/3d79bdf0f7049c209b4659ff8c418a1b859d7cfa/gnomad_qc/v2/annotations/generate_qc_annotations.py
     '''
-    fam_ht = read_fam(fam_file)
+    fam_ht = read_fam(path_spark(fam_file))
     return mt.annotate_cols(unrelated_sample=hl.is_missing(fam_ht[mt.s]))
 
 
@@ -135,11 +135,11 @@ def generate_family_stats(mt: hl.MatrixTable, fam_file: str, calculate_adj: bool
     """
     #mt = mt.select_cols(high_quality=mt.meta.high_quality)
     mt = mt.select_rows()
-    mt = annotate_unrelated_sample(mt, fam_file)
+    mt = annotate_unrelated_sample(mt, path_spark(fam_file))
 
     # Unphased for now, since mendel_errors does not support phased alleles
     mt = mt.annotate_entries(GT=unphase_call_expr(mt.GT))
-    ped = hl.Pedigree.read(fam_file, delimiter='\\t')
+    ped = hl.Pedigree.read(path_spark(fam_file), delimiter='\\t')
     family_stats_struct, family_stats_sample_ht = family_stats(mt, ped, 'raw')
     mt = mt.annotate_rows(family_stats=[family_stats_struct])
 
@@ -190,7 +190,9 @@ def generate_trio_stats(
     return ht
 
 
-def trio_family_dnm_annotation(varqc_mtfile: str, pedfile: str, trio_mtfile: str, trio_stats_htfile: str, fam_stats_htfile: str, fam_stats_mtfile: str, fam_stats_gnomad_mtfile: str, gnomad_htfile: str, dnm_htfile: str):
+def trio_family_dnm_annotation(varqc_mtfile: str, pedfile: str, trio_mtfile: str, 
+                               trio_stats_htfile: str, fam_stats_htfile: str, fam_stats_mtfile: str, 
+                               fam_stats_gnomad_mtfile: str, gnomad_htfile: str, dnm_htfile: str) -> None:
     '''
     Create matrixtable of just trios, create family stats
     :param str varqc_mtfile: Input matrixtable file
@@ -203,8 +205,8 @@ def trio_family_dnm_annotation(varqc_mtfile: str, pedfile: str, trio_mtfile: str
     :param str gnomad_htfile: Gnomad AF hail table
     :param str dnm_htfile: De novo hail table file
     '''
-    pedigree = hl.Pedigree.read(pedfile)
-    mt = hl.read_matrix_table(varqc_mtfile)
+    pedigree = hl.Pedigree.read(path_spark(pedfile))
+    mt = hl.read_matrix_table(path_spark(varqc_mtfile))
 
     #filter mt to samples that are in trios only and re-run varqc
     trio_sample_ht = hl.import_fam(pedfile)
@@ -213,25 +215,25 @@ def trio_family_dnm_annotation(varqc_mtfile: str, pedfile: str, trio_mtfile: str
     mt2 = hl.variant_qc(mt2, name = 'varqc_trios')
 
     trio_dataset = hl.trio_matrix(mt2, pedigree, complete_trios=True)
-    trio_dataset.write(trio_mtfile, overwrite=True)
+    trio_dataset.write(path_spark(trio_mtfile), overwrite=True)
 
     trio_stats_ht = generate_trio_stats(trio_dataset, autosomes_only=True, bi_allelic_only=True)
-    trio_stats_ht.write(trio_stats_htfile, overwrite=True)
+    trio_stats_ht.write(path_spark(trio_stats_htfile), overwrite=True)
 
     print("Generating family stats")
     (ht1, famstats_ht) = generate_family_stats(mt, pedfile)
-    ht1.write(fam_stats_htfile ,overwrite=True)
+    ht1.write(path_spark(fam_stats_htfile) ,overwrite=True)
 
     mt = mt.annotate_rows(family_stats=ht1[mt.row_key].family_stats)
-    mt.write(fam_stats_mtfile , overwrite=True)
+    mt.write(path_spark(fam_stats_mtfile) , overwrite=True)
     #add gnomad AFs
-    gnomad_ht = hl.read_table(gnomad_htfile)
+    gnomad_ht = hl.read_table(path_spark(gnomad_htfile))
     mt = mt.annotate_rows(gnomad_maf=gnomad_ht[mt.row_key].freq[0].AF)
-    mt.write(fam_stats_gnomad_mtfile, overwrite=True)
+    mt.write(path_spark(fam_stats_gnomad_mtfile), overwrite=True)
     #make DNM table
     de_novo_table = hl.de_novo(mt, pedigree, mt.gnomad_maf)
     de_novo_table = de_novo_table.key_by('locus', 'alleles').collect_by_key('de_novo_data')
-    de_novo_table.write(dnm_htfile, overwrite=True)
+    de_novo_table.write(path_spark(dnm_htfile), overwrite=True)
 
 
 def generate_allele_data(mt: hl.MatrixTable) -> hl.Table:
@@ -286,7 +288,7 @@ def create_inbreeding_ht_with_ac_and_allele_data(varqc_mtfile: str, inbreeding_h
     :param str qc_ac_htfile: qc_ac hail table file
     :param str allele_data_htfile: Allele data htfile
     '''
-    mt = hl.read_matrix_table(varqc_mtfile)
+    mt = hl.read_matrix_table(path_spark(varqc_mtfile))
     # inbreeding ht
     mt_inbreeding = mt.annotate_rows(InbreedingCoeff=bi_allelic_site_inbreeding_expr(mt.GT))
     mt = mt.key_rows_by('locus').distinct_by_row().key_rows_by('locus', 'alleles')
@@ -295,60 +297,48 @@ def create_inbreeding_ht_with_ac_and_allele_data(varqc_mtfile: str, inbreeding_h
     allele_data_ht = generate_allele_data(mt)
     qc_ac_ht = generate_ac(mt)
     # write to file
-    ht_inbreeding.write(inbreeding_htfile , overwrite=True)
-    qc_ac_ht.write(qc_ac_htfile , overwrite=True)
-    allele_data_ht.write(allele_data_htfile, overwrite=True)
+    ht_inbreeding.write(path_spark(inbreeding_htfile) , overwrite=True)
+    qc_ac_ht.write(path_spark(qc_ac_htfile) , overwrite=True)
+    allele_data_ht.write(path_spark(allele_data_htfile), overwrite=True)
 
 
 def main():
-    #set up
+    # set up
     args = get_options()
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
-    resourcedir = inputs['resource_dir']
-    training_sets_dir = inputs['training_set_dir']
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
+    resourcedir = config['general']['resource_dir']
+    training_sets_dir = config['general']['training_sets_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
     # get truth set ht
-    truth_ht_file = resourcedir + "truthset_table.ht"
     if args.truth or args.all:
-        omni = training_sets_dir + "1000G_omni2.5.hg38.ht"
-        mills = training_sets_dir + "Mills_and_1000G_gold_standard.indels.hg38.ht"
-        thousand_genomes = training_sets_dir + "1000G_phase1.snps.high_confidence.hg38.ht"
-        hapmap = training_sets_dir + "hapmap_3.3.hg38.ht"
-        get_truth_ht(omni, mills, thousand_genomes, hapmap, truth_ht_file)
+        truth_ht_outfile = config['step3']['get_truth_ht']['truth_ht_outfile']
+        omni = config['step3']['get_truth_ht']['omni']
+        mills = config['step3']['get_truth_ht']['mills']
+        thousand_genomes = config['step3']['get_truth_ht']['thousand_genomes']
+        hapmap = config['step3']['get_truth_ht']['hapmap']
+        get_truth_ht(omni, mills, thousand_genomes, hapmap, truth_ht_outfile)
 
     #add hail variant QC
     if args.annotation or args.all:
-        #mtfile = mtdir + "mt_pops_QC_filters_sequencing_location_and_superpop_sanger_only_after_sample_qc.mt"
+        # mtfile = mtdir + "mt_pops_QC_filters_sequencing_location_and_superpop_sanger_only_after_sample_qc.mt"
         # mtfile = mtdir + "gatk_calls_from_broad.mt"
-        mtfile = mtdir + "gatk_broad_crams_sanger_calls.mt"
-        varqc_mtfile = mtdir + "mt_varqc.mt"
-        varqc_mtfile_split = mtdir + "mt_varqc_splitmulti.mt"
-
-        split_multi_and_var_qc(mtfile, varqc_mtfile, varqc_mtfile_split)
-        # pedfile = resourcedir + "trios.ped"
-
-        #get complete trios, family annotation, dnm annotation
-        # trio_mtfile = mtdir + "trios.mt"
-        # trio_stats_htfile = mtdir + "trio_stats.ht"
-        # fam_stats_htfile = mtdir + "family_stats.ht"
-        # fam_stats_mtfile = mtdir + "family_stats.mt"
-        # fam_stats_gnomad_mtfile = mtdir + "family_stats_gnomad.mt"
-        # gnomad_htfile = resourcedir + "gnomad.exomes.r2.1.1.sites.liftover_grch38.ht"
-        # dnm_htfile = mtdir + "denovo_table.ht"
-        # trio_family_dnm_annotation(varqc_mtfile_split, pedfile, trio_mtfile, trio_stats_htfile, fam_stats_htfile, fam_stats_mtfile, fam_stats_gnomad_mtfile, gnomad_htfile, dnm_htfile)
+        mtfile = config['step3']['split_multi_and_var_qc']['mtfile']
+        varqc_mtoutfile = config['step3']['split_multi_and_var_qc']['varqc_mtoutfile']
+        varqc_mtoutfile_split = config['step3']['split_multi_and_var_qc']['varqc_mtoutfile_split']
+        split_multi_and_var_qc(mtfile, varqc_mtoutfile, varqc_mtoutfile_split)
 
         #create inbreeding ht
-        inbreeding_htfile = mtdir + "inbreeding.ht"
-        qc_ac_htfile = mtdir + "qc_ac.ht"
-        allele_data_htfile = mtdir + "allele_data.ht"
-        create_inbreeding_ht_with_ac_and_allele_data(varqc_mtfile, inbreeding_htfile, qc_ac_htfile, allele_data_htfile)
+        inbreeding_htoutfile = config['step3']['create_inbreeding_ht_with_ac_and_allele_data']['inbreeding_htoutfile']
+        qc_ac_htoutfile = config['step3']['create_inbreeding_ht_with_ac_and_allele_data']['qc_ac_htoutfile']
+        allele_data_htoutfile = config['step3']['create_inbreeding_ht_with_ac_and_allele_data']['allele_data_htoutfile']
+        create_inbreeding_ht_with_ac_and_allele_data(varqc_mtoutfile, inbreeding_htoutfile, qc_ac_htoutfile, allele_data_htoutfile)
 
 
 if __name__ == '__main__':
diff --git a/3-variant_qc/variant_qc_non_trios/2-create_rf_ht_non_trios.py b/3-variant_qc/variant_qc_non_trios/2-create_rf_ht_non_trios.py
index 837c313..b2e61dc 100755
--- a/3-variant_qc/variant_qc_non_trios/2-create_rf_ht_non_trios.py
+++ b/3-variant_qc/variant_qc_non_trios/2-create_rf_ht_non_trios.py
@@ -1,12 +1,14 @@
-#create hail table for random forest
+# create hail table for random forest
 import hail as hl
 import pyspark
-import wes_qc.utils.constants as constants
-from wes_qc.utils.utils import parse_config
+import utils.constants as constants
+from utils.utils import parse_config, path_spark, path_local
 from gnomad.variant_qc.random_forest import median_impute_features
 
 
-def create_rf_ht(mtfile: str, truthset_file: str, allele_data_file: str, allele_counts_file: str, inbreeding_file: str, htfile_rf_all_cols: str, htfile_rf_var_type_all_cols: str):
+def create_rf_ht(mtfile: str, truthset_file: str, allele_data_file: str, 
+                 allele_counts_file: str, inbreeding_file: str, 
+                 htfile_rf_all_cols: str, htfile_rf_var_type_all_cols: str, config: dict) -> None:
     '''
     Load input mt and training data to create an input for random forest
     param str mtfile: Input matrixtable file
@@ -17,12 +19,14 @@ def create_rf_ht(mtfile: str, truthset_file: str, allele_data_file: str, allele_
     param str htfile_rf_all_cols: Output file for RF hail table 
     param str htfile_rf_var_type_all_cols: Output file for RF hail table by variant type
     '''
+    conf = config['step3']['create_rf_ht']
+
     n_partitions = 200
-    mt = hl.read_matrix_table(mtfile)
-    truth_data_ht = hl.read_table(truthset_file)
-    allele_data_ht = hl.read_table(allele_data_file)
-    allele_counts_ht = hl.read_table(allele_counts_file)
-    inbreeding_ht = hl.read_table(inbreeding_file)
+    mt = hl.read_matrix_table(path_spark(mtfile))
+    truth_data_ht = hl.read_table(path_spark(truthset_file))
+    allele_data_ht = hl.read_table(path_spark(allele_data_file))
+    allele_counts_ht = hl.read_table(path_spark(allele_counts_file))
+    inbreeding_ht = hl.read_table(path_spark(inbreeding_file))
 
     allele_counts_ht = allele_counts_ht.select(*['ac_qc_samples_raw', 'ac_qc_samples_adj'])
     group = "raw"
@@ -54,8 +58,8 @@ def create_rf_ht(mtfile: str, truthset_file: str, allele_data_file: str, allele_
     # ht = ht.annotate(is_CG=((ht.alleles[0] == "C") & (ht.alleles[1] == "G")) | ((ht.alleles[0] == "G") & (ht.alleles[1] == "C")))
     # ht = ht.annotate(is_CT=((ht.alleles[0] == "C") & (ht.alleles[1] == "T")) | ((ht.alleles[0] == "G") & (ht.alleles[1] == "A")))
 
-    ht = ht.annotate(fail_hard_filters=(ht.QD < 2)
-                     | (ht.FS > 60) | (ht.MQ < 30))
+    ht = ht.annotate(fail_hard_filters=(ht.QD < conf['fail_hard_filters_QD_less_than'])
+                     | (ht.FS > conf['fail_hard_filters_FS_greater_than']) | (ht.MQ < conf['fail_hard_filters_MQ_less_than']))
     ht = ht.annotate(ac_raw=ht.ac_qc_samples_raw)
     # ht = ht.annotate(transmitted_singleton=(
     #     ht[f"n_transmitted_{group}"] == 1) & (ht[f"ac_qc_samples_{group}"] == 2))
@@ -68,41 +72,43 @@ def create_rf_ht(mtfile: str, truthset_file: str, allele_data_file: str, allele_
         **{
             # "transmitted_singleton": (ht[f"n_transmitted_{group}"] == 1)
             # & (ht[f"ac_qc_samples_{group}"] == 2),
-            "fail_hard_filters": (ht.QD < 2) | (ht.FS > 60) | (ht.MQ < 30),
+            "fail_hard_filters": (ht.QD < conf['fail_hard_filters_QD_less_than']) | (ht.FS > conf['fail_hard_filters_FS_greater_than']) | (ht.MQ < conf['fail_hard_filters_MQ_less_than']),
         },
         ac_raw=ht.ac_qc_samples_raw
     )
 
     ht = ht.repartition(n_partitions, shuffle=False)
-    ht = ht.checkpoint(htfile_rf_all_cols, overwrite=True)
+    ht = ht.checkpoint(path_spark(htfile_rf_all_cols), overwrite=True)
     ht = median_impute_features(ht, strata={"variant_type": ht.variant_type})
-    ht = ht.checkpoint(htfile_rf_var_type_all_cols, overwrite=True)
+    ht = ht.checkpoint(path_spark(htfile_rf_var_type_all_cols), overwrite=True)
 
 
 def main():
-    #set up
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
-    resourcedir = inputs['resource_dir']
+    # set up
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
+    resourcedir = config['general']['resource_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
-
-    truthset_file = resourcedir + "truthset_table.ht"
-    # trio_stats_file = mtdir + "trio_stats.ht"
-    allele_data_file = mtdir + "allele_data.ht"
-    allele_counts_file = mtdir + "qc_ac.ht"
-    inbreeding_file = mtdir + "inbreeding.ht"
-
-   #mtfile = mtdir + "mt_pops_QC_filters_sequencing_location_and_superpop_sanger_only_after_sample_qc.mt"
-    mtfile = mtdir + "mt_varqc_splitmulti.mt"
-    htfile_rf_all_cols = mtdir + "ht_for_RF_all_cols.ht"
-    htfile_rf_var_type_all_cols = mtdir + "ht_for_RF_by_variant_type_all_cols.ht"
-
-    create_rf_ht(mtfile, truthset_file, allele_data_file, allele_counts_file, inbreeding_file, htfile_rf_all_cols, htfile_rf_var_type_all_cols)
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
+
+    truthset_file = config['step3']['create_rf_ht']['truthset_file']
+    allele_data_file = config['step3']['create_rf_ht']['allele_data_file']
+    allele_counts_file = config['step3']['create_rf_ht']['allele_counts_file']
+    inbreeding_file = config['step3']['create_rf_ht']['inbreeding_file']
+
+    # mtfile = mtdir + "mt_pops_QC_filters_sequencing_location_and_superpop_sanger_only_after_sample_qc.mt"
+    mtfile = config['step3']['create_rf_ht']['mtfile']
+    htoutfile_rf_all_cols = config['step3']['create_rf_ht']['htoutfile_rf_all_cols']
+    htoutfile_rf_var_type_all_cols = config['step3']['create_rf_ht']['htoutfile_rf_var_type_all_cols']
+
+    create_rf_ht(mtfile, truthset_file, 
+                 allele_data_file, allele_counts_file, 
+                 inbreeding_file, htoutfile_rf_all_cols, 
+                 htoutfile_rf_var_type_all_cols, config)
 
 
 if __name__ == '__main__':
diff --git a/3-variant_qc/variant_qc_non_trios/5-annotate_ht_after_rf_no_trios.py b/3-variant_qc/variant_qc_non_trios/5-annotate_ht_after_rf_no_trios.py
index 169cf88..3d4a933 100755
--- a/3-variant_qc/variant_qc_non_trios/5-annotate_ht_after_rf_no_trios.py
+++ b/3-variant_qc/variant_qc_non_trios/5-annotate_ht_after_rf_no_trios.py
@@ -1,8 +1,9 @@
 # this is a copy of the annotation script to use when there are mo trios and therefore no transmitted/unstransmitted ratios can be calculated
+import os
 import hail as hl
 import pyspark
 import argparse
-from wes_qc.utils.utils import parse_config
+from utils.utils import parse_config, path_spark, path_local
 
 
 def get_options():
@@ -26,7 +27,9 @@ def add_cq_annotation(htfile: str, synonymous_file: str, ht_cq_file: str):
     ;param str synonymous_file: text file containing synonymous variants
     ;param str ht_cq_fle: Output hail table file annotated with synonymous variants
     '''
-    synonymous_ht=hl.import_table(synonymous_file,types={'f0':'str','f1':'int32', 'f2':'str','f3':'str','f4':'str', 'f5':'str'}, no_header=True)
+    synonymous_ht=hl.import_table(path_spark(synonymous_file), 
+                                  types={'f0':'str','f1':'int32', 'f2':'str','f3':'str','f4':'str', 'f5':'str'},
+                                  no_header=True)
     synonymous_ht=synonymous_ht.annotate(chr=synonymous_ht.f0)
     synonymous_ht=synonymous_ht.annotate(pos=synonymous_ht.f1)
     synonymous_ht=synonymous_ht.annotate(rs=synonymous_ht.f2)
@@ -38,9 +41,9 @@ def add_cq_annotation(htfile: str, synonymous_file: str, ht_cq_file: str):
     synonymous_ht=synonymous_ht.drop(synonymous_ht.f0,synonymous_ht.f1,synonymous_ht.f2,synonymous_ht.f3,synonymous_ht.f4,synonymous_ht.chr,synonymous_ht.pos,synonymous_ht.ref,synonymous_ht.alt)
     synonymous_ht = synonymous_ht.key_by(synonymous_ht.locus, synonymous_ht.alleles)
 
-    ht = hl.read_table(htfile)
+    ht = hl.read_table(path_spark(htfile))
     ht=ht.annotate(consequence=synonymous_ht[ht.key].consequence)
-    ht.write(ht_cq_file, overwrite=True)
+    ht.write(path_spark(ht_cq_file), overwrite=True)
 
 
 def dnm_and_family_annotation(ht_cq_fle: str, dnm_htfile: str, fam_stats_htfile: str, trio_stats_htfile: str, family_annot_htfile: str):
@@ -52,14 +55,14 @@ def dnm_and_family_annotation(ht_cq_fle: str, dnm_htfile: str, fam_stats_htfile:
     :param str trio_stats_htfile: Trio stats hail table file
     :param str family_annot_htfile: Output hail table annotated with DNMs and family stats file
     '''
-    ht = hl.read_table(ht_cq_fle)
-    dnm_ht = hl.read_table(dnm_htfile)
-    fam_stats_ht = hl.read_table(fam_stats_htfile)
-    trio_stats_ht = hl.read_table(trio_stats_htfile)
+    ht = hl.read_table(path_spark(ht_cq_fle))
+    dnm_ht = hl.read_table(path_spark(dnm_htfile))
+    fam_stats_ht = hl.read_table(path_spark(fam_stats_htfile))
+    trio_stats_ht = hl.read_table(path_spark(trio_stats_htfile))
     ht=ht.annotate(de_novo_data=dnm_ht[ht.key].de_novo_data)
     ht=ht.annotate(family_stats=fam_stats_ht[ht.key].family_stats)
     ht=ht.annotate(fam=trio_stats_ht[ht.key])
-    ht.write(family_annot_htfile, overwrite=True)
+    ht.write(path_spark(family_annot_htfile), overwrite=True)
 
 
 def count_trans_untransmitted_singletons(mt_filtered: hl.MatrixTable, ht: hl.Table) -> hl.Table:
@@ -126,8 +129,8 @@ def transmitted_singleton_annotation(family_annot_htfile: str, trio_mtfile: str,
     :param str trans_sing_htfile: Variant QC hail table file with transmitted singleton annotation
     '''
     print("Annotating with transmitted singletons")
-    ht = hl.read_table(family_annot_htfile)
-    mt_trios = hl.read_matrix_table(trio_mtfile)
+    ht = hl.read_table(path_spark(family_annot_htfile))
+    mt_trios = hl.read_matrix_table(path_spark(trio_mtfile))
     mt_trios = mt_trios.annotate_rows(consequence=ht[mt_trios.row_key].consequence)
     #there is a save step here in Pavlos file, is it needed?
     mt_filtered = mt_trios.filter_rows((mt_trios.info.AC[0] <= 2) & (mt_trios.consequence == "synonymous_variant"))
@@ -135,7 +138,7 @@ def transmitted_singleton_annotation(family_annot_htfile: str, trio_mtfile: str,
     mt_filtered.write(trio_filtered_mtfile, overwrite=True)
 
     ht = count_trans_untransmitted_singletons(mt_filtered, ht)
-    ht.write(trans_sing_htfile, overwrite=True)    
+    ht.write(path_spark(trans_sing_htfile), overwrite=True)    
 
 
 # def run_tdt(mtfile: str, trans_sing_htfile: str, pedfile: str, tdt_htfile: str):
@@ -165,54 +168,36 @@ def annotate_gnomad(tdt_htfile: str, gnomad_htfile: str, final_htfile: str):
     :param str final_htfile: Final RF htfile for ranking and binning
     '''
     print("Annotating with gnomad AF")
-    ht = hl.read_table(tdt_htfile)
-    gnomad_ht = hl.read_table(gnomad_htfile)
-    ht = ht.annotate(gnomad_af=gnomad_ht[ht.key].maf)
-    ht.write(final_htfile, overwrite = True)
+    ht = hl.read_table(path_spark(tdt_htfile))
+    gnomad_ht = hl.read_table(path_spark(gnomad_htfile))
+    ht = ht.annotate(gnomad_af=gnomad_ht[ht.key].faf) # DEBUG: maf or faf? maf results in an error for me
+    ht.write(path_spark(final_htfile), overwrite = True)
 
 
 def main():
     # set up
     args = get_options()
-    inputs = parse_config()
-    rf_dir = inputs['var_qc_rf_dir']
-    mtdir = inputs['matrixtables_lustre_dir']
-    resourcedir = inputs['resource_dir']
+    config = parse_config()
+    rf_dir = path_spark(config['general']['var_qc_rf_dir']) # TODO: add adapters inside the functions to enhance robustness
+    mtdir = config['general']['matrixtables_dir']
+    resourcedir = config['general']['resource_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
-    htfile = rf_dir + args.runhash + "/rf_result.ht"
+    # TODO move runhash from cli to config
+    htfile = os.path.join(rf_dir, args.runhash, "rf_result.ht")
     #annotate with synonymous CQs
-    synonymous_file = resourcedir + "synonymous_variants.txt"
-    ht_cq_file = rf_dir + args.runhash + "/rf_result_with_synonymous.ht"
+    synonymous_file = config['step3']['add_cq_annotation']['synonymous_file']
+    ht_cq_file = os.path.join(rf_dir, args.runhash, "rf_result_with_synonymous.ht")
     add_cq_annotation(htfile, synonymous_file, ht_cq_file)
-    #annotate with family stats and DNMs
-    # dnm_htfile = mtdir + "denovo_table.ht"
-    # fam_stats_htfile = mtdir + "family_stats.ht"
-    # trio_stats_htfile = mtdir + "trio_stats.ht"
-    # family_annot_htfile = rf_dir + args.runhash + "/rf_result_denovo_family_stats.ht"
-    # dnm_and_family_annotation(ht_cq_file, dnm_htfile, fam_stats_htfile, trio_stats_htfile, family_annot_htfile)
-
-    #annotate with transmitted singletons
-    # trio_mtfile = mtdir + "trios.mt"
-    # trio_filtered_mtfile = mtdir + "trios_filtered_.mt"
-    # trans_sing_htfile = rf_dir + args.runhash + "/rf_result_trans_sing.ht"
-    # transmitted_singleton_annotation(family_annot_htfile, trio_mtfile, trio_filtered_mtfile, trans_sing_htfile)
-
-    #annotate with number transmitted, number untransmitted (from transmission disequilibrium test)
-    # mtfile = mtdir + "mt_varqc_splitmulti.mt"
-    # pedfile = resourcedir + "trios.ped"
-    # tdt_htfile = rf_dir + args.runhash + "/rf_result_tdt.ht"
-    # run_tdt(mtfile, trans_sing_htfile, pedfile, tdt_htfile)
 
     #annotate with gnomad AF
-    final_htfile = rf_dir + args.runhash + "/rf_result_final_for_ranking.ht"
-    gnomad_htfile = resourcedir + "gnomad_v3-0_AF.ht"
-    #annotate_gnomad(trans_sing_htfile, gnomad_htfile, final_htfile)
+    final_htfile = os.path.join(rf_dir, args.runhash, "rf_result_final_for_ranking.ht")
+    gnomad_htfile = config['step3']['annotate_gnomad']['gnomad_htfile']
     annotate_gnomad(ht_cq_file, gnomad_htfile, final_htfile)
 
 
diff --git a/3-variant_qc/variant_qc_non_trios/6-rank_and_bin_no_trios.py b/3-variant_qc/variant_qc_non_trios/6-rank_and_bin_no_trios.py
index d642274..9c181f8 100755
--- a/3-variant_qc/variant_qc_non_trios/6-rank_and_bin_no_trios.py
+++ b/3-variant_qc/variant_qc_non_trios/6-rank_and_bin_no_trios.py
@@ -1,11 +1,12 @@
 # rank and bin RF output
 #copy of the original for a cohort with no trios so no transmitted/untransmitted can be calculated
+import os
 import hail as hl
 import pyspark
 import argparse
 from typing import Optional, Dict
 from pprint import pformat
-from wes_qc.utils.utils import parse_config
+from utils.utils import parse_config, path_spark, path_local
 
 
 def get_options():
@@ -96,7 +97,7 @@ def add_rank(
     return ht
 
 
-def create_binned_data_initial(ht: hl.Table, bin_tmp_htfile: str, truth_htfile: str, n_bins: int) -> hl.Table:
+def create_binned_data_initial(ht: hl.Table, bin_tmp_htfile: str, truth_htfile: str, n_bins: int, config: dict) -> hl.Table:
     '''
     Create binned data from RF
     :param hl.Table ht: Input hail table
@@ -105,6 +106,8 @@ def create_binned_data_initial(ht: hl.Table, bin_tmp_htfile: str, truth_htfile:
     :param int n_bins: Number of bins to create
     :return: Table with bins added
     '''
+    conf = config['step3']['create_binned_data_initial'] # not used in non-trios
+
     # Count variants for ranking
     # count_expr = {x: hl.agg.filter(hl.is_defined(ht[x]), hl.agg.counter(hl.cond(hl.is_snp(
     #     ht.alleles[0], ht.alleles[1]), 'snv', 'indel'))) for x in ht.row if x.endswith('rank')}
@@ -113,7 +116,7 @@ def create_binned_data_initial(ht: hl.Table, bin_tmp_htfile: str, truth_htfile:
     rank_variant_counts = ht.aggregate(hl.Struct(**count_expr))
     print(f"Found the following variant counts:\n {pformat(rank_variant_counts)}")
 
-    ht_truth_data = hl.read_table(truth_htfile)
+    ht_truth_data = hl.read_table(path_spark(truth_htfile))
     ht = ht.annotate_globals(rank_variant_counts=rank_variant_counts)
     # ht = ht.annotate(
     #     **ht_truth_data[ht.key],
@@ -157,7 +160,7 @@ def create_binned_data_initial(ht: hl.Table, bin_tmp_htfile: str, truth_htfile:
     )
     ht = ht.filter(hl.is_defined(ht.bin))
 
-    ht = ht.checkpoint(bin_tmp_htfile, overwrite=True)
+    ht = ht.checkpoint(path_spark(bin_tmp_htfile), overwrite=True)
 
     # Create binned data
     return (
@@ -267,20 +270,21 @@ def create_binned_data_initial(ht: hl.Table, bin_tmp_htfile: str, truth_htfile:
 def main():
     # set up
     args = get_options()
-    inputs = parse_config()
-    rf_dir = inputs['var_qc_rf_dir']
-    resourcedir = inputs['resource_dir']
+    config = parse_config()
+    rf_dir = path_spark(config['general']['var_qc_rf_dir']) # TODO: add adapters inside the functions to enhance robustness
+    resourcedir = config['general']['resource_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
     # add rank
-    htfile = rf_dir + args.runhash + "/rf_result_final_for_ranking.ht"
-    htrankedfile = rf_dir + args.runhash + "/rf_result_ranked.ht"
-    ht = hl.read_table(htfile)
+    htfile = os.path.join(rf_dir, args.runhash, "rf_result_final_for_ranking.ht")
+    htrankedfile = os.path.join(rf_dir, args.runhash, "rf_result_ranked.ht")
+
+    ht = hl.read_table(path_spark(htfile))
     ht_ranked = add_rank(ht,
                         score_expr=(1-ht.rf_probability["TP"]),
                         subrank_expr={
@@ -293,13 +297,13 @@ def main():
                         }
                         )
     ht_ranked = ht_ranked.annotate(score=(1-ht_ranked.rf_probability["TP"]))
-    ht_ranked.write(htrankedfile, overwrite=True)
+    ht_ranked.write(path_spark(htrankedfile), overwrite=True)
     # add bins
-    truth_htfile = resourcedir + "truthset_table.ht"
-    bin_tmp_htfile = rf_dir + args.runhash + "/_gnomad_score_binning_tmp.ht"
-    ht_bins = create_binned_data_initial(ht_ranked, bin_tmp_htfile, truth_htfile, n_bins=100)
-    bin_htfile = rf_dir + args.runhash + "/_rf_result_ranked_BINS.ht"
-    ht_bins.write(bin_htfile, overwrite=True)
+    truth_htfile = config['step3']['create_binned_data_initial']['truth_htfile']
+    bin_tmp_htfile = os.path.join(rf_dir, args.runhash, "_gnomad_score_binning_tmp.ht")
+    ht_bins = create_binned_data_initial(ht_ranked, bin_tmp_htfile, truth_htfile, n_bins=100, config=config)
+    bin_htfile = os.path.join(rf_dir, args.runhash, "_rf_result_ranked_BINS.ht")
+    ht_bins.write(path_spark(bin_htfile), overwrite=True)
 
 
 if __name__ == '__main__':
diff --git a/3-variant_qc/variant_qc_non_trios/7-plot_rf_output_no_trios.py b/3-variant_qc/variant_qc_non_trios/7-plot_rf_output_no_trios.py
index d68fa09..efca817 100755
--- a/3-variant_qc/variant_qc_non_trios/7-plot_rf_output_no_trios.py
+++ b/3-variant_qc/variant_qc_non_trios/7-plot_rf_output_no_trios.py
@@ -1,15 +1,20 @@
+# TODO: fix bokeh Deprecation Warnings
+
 # create plots from binned random forest output
 import hail as hl
 import pyspark
 import os
 import argparse
 import pandas as pd
-from typing import Union, Dict, List, Set, Tuple
-from bokeh.models import Plot, Row, Span
-from bokeh.plotting import output_file, save
+import numpy as np
+from typing import Union, Dict, List, Set, Tuple, Callable
+import bokeh.models as bm
+
+from bokeh.models.layouts import TabPanel, Tabs
+from bokeh.plotting import output_file, save, figure
 from gnomad.utils.plotting import *
 from hail.plot import show, output_notebook
-from wes_qc.utils.utils import parse_config
+from utils.utils import parse_config, path_spark, path_local
 
 
 def get_options():
@@ -26,12 +31,12 @@ def get_options():
     return args
 
 
-def set_plots_defaults(p: Plot, qc_plots_settings: dict) -> None:
+def set_plots_defaults(p: bm.Plot, qc_plots_settings: dict) -> None:
     p.legend.label_text_font_size = qc_plots_settings['label_text_font_size']
-    p.title.text_font_size = qc_plots_settings['title.text_font_size']
-    p.axis.axis_label_text_font_size = qc_plots_settings['axis.axis_label_text_font_size']
-    p.axis.axis_label_text_font_style = qc_plots_settings['axis.axis_label_text_font_style']
-    p.axis.major_label_text_font_size = qc_plots_settings['axis.major_label_text_font_size']
+    p.title.text_font_size = qc_plots_settings['title_text_font_size']
+    p.axis.axis_label_text_font_size = qc_plots_settings['axis_axis_label_text_font_size']
+    p.axis.axis_label_text_font_style = qc_plots_settings['axis_axis_label_text_font_style']
+    p.axis.major_label_text_font_size = qc_plots_settings['axis_major_label_text_font_size']
 
     
 def get_point_size_col(data: pd.Series, size_prop: str, qc_plots_settings: dict) -> pd.Series:
@@ -109,7 +114,7 @@ def plot_metric(df: pd.DataFrame,
     :return: Plot
     :rtype: Tabs
     """
-    def get_row(df: pd.DataFrame, y_name: str, cols: List[str], y_fun: Callable[[pd.Series], Union[float, int]], titles: List[str], link_cumul_y: bool, cut: int = None) -> Row:
+    def get_row(df: pd.DataFrame, y_name: str, cols: List[str], y_fun: Callable[[pd.Series], Union[float, int]], titles: List[str], link_cumul_y: bool, cut: int = None) -> bm.Row:
         """
         Generates a single row with two plots: a regular scatter plot and a cumulative one.
         Both plots have bins on the x-axis. The y-axis is computed by applying the function `y_fun` on the columns `cols`.
@@ -120,7 +125,7 @@ def get_row(df: pd.DataFrame, y_name: str, cols: List[str], y_fun: Callable[[pd.
 
         """
 
-        def get_plot(data_source: ColumnDataSource, y_name: str, y_col_name: str, titles: List[str], data_ranges: Tuple[DataRange1d, DataRange1d], cut: int = None) -> Plot:
+        def get_plot(data_source: ColumnDataSource, y_name: str, y_col_name: str, titles: List[str], data_ranges: Tuple[DataRange1d, DataRange1d], cut: int = None) -> bm.Plot:
             """
             Generates a single scatter plot panel
             """
@@ -134,7 +139,7 @@ def get_plot(data_source: ColumnDataSource, y_name: str, y_col_name: str, titles
             p.y_range = data_ranges[1]
 
             if cut:
-                p.add_layout(Span(location=cut, dimension='height', line_color='red', line_dash='dashed'))
+                p.add_layout(bm.Span(location=cut, dimension='height', line_color='red', line_dash='dashed'))
 
             # Add circles layouts one model at a time, so that no default legend is generated.
             # Because data is in the same ColumnDataSource, use a BooleanFilter to plot each model separately
@@ -158,15 +163,19 @@ def get_plot(data_source: ColumnDataSource, y_name: str, y_col_name: str, titles
 
             # Add subtitles if any
             for title in titles[1:]:
-                p.add_layout(Title(text=title, text_font_size=qc_plots_settings['subtitle.text_font_size']), 'above')
+                p.add_layout(Title(text=title, text_font_size=qc_plots_settings['subtitle_text_font_size']), 'above')
 
             return p
         # Compute non-cumulative values by applying `y_fun`
         df['non_cumul'] = df[cols].apply(y_fun, axis=1)
 
+        # TODO: check if the result is the same after refactoring
         # Compute cumulative values for each of the data columns
         for col in cols:
-            df[f'{col}_cumul'] = df.groupby('model').aggregate(np.cumsum)[col]
+            # skip non-numeric colums
+            if pd.api.types.is_numeric_dtype(df[col]):
+                df[f'{col}_cumul'] = df.groupby('model')[col].cumsum()
+
         df['cumul'] = df[[f'{col}_cumul' for col in cols]].apply(y_fun, axis=1)
 
         # Create data ranges that are either shared or distinct depending on the y_cumul parameter
@@ -174,7 +183,7 @@ def get_plot(data_source: ColumnDataSource, y_name: str, y_col_name: str, titles
         cumul_data_ranges = non_cumul_data_ranges if link_cumul_y else (non_cumul_data_ranges[0], DataRange1d())
         data_source = ColumnDataSource(df)
 
-        return Row(get_plot(data_source, y_name, 'non_cumul', titles, non_cumul_data_ranges, cut),
+        return bm.Row(get_plot(data_source, y_name, 'non_cumul', titles, non_cumul_data_ranges, cut),
                    get_plot(data_source, y_name, 'cumul', [titles[0] + ', cumulative'] + titles[1:], cumul_data_ranges, cut))
 
     
@@ -209,7 +218,7 @@ def prepare_pd(df: pd.DataFrame, cols: List[str], colors: Dict[str, str] = {}, s
                 print('No data found for plot: {}'.format('\t'.join(titles)))
 
         if children:
-            tabs.append(Panel(child=Column(children=children), title='All'))
+            tabs.append(TabPanel(child=Column(children=children), title='All'))
 
    
     if plot_singletons:
@@ -224,7 +233,7 @@ def prepare_pd(df: pd.DataFrame, cols: List[str], colors: Dict[str, str] = {}, s
                     print('No data found for plot: {}'.format('\t'.join(titles)))
 
         if children:
-            tabs.append(Panel(child=Column(children=children), title='Singletons'))
+            tabs.append(TabPanel(child=Column(children=children), title='Singletons'))
 
     return Tabs(tabs=tabs)
 
@@ -354,26 +363,29 @@ def create_plots(bin_htfile: str, plot_dir: str, run_hash: str, qc_plots_setting
 def main():
     # set up
     args = get_options()
-    inputs = parse_config()
-    rf_dir = inputs['var_qc_rf_dir']
-    root_plot_dir = inputs['plots_dir_local']
-
-    qc_plots_settings = {
-    'mean_point_size': 4.0,
-    'min_point_size': 1.0,
-    'max_point_size': 16.0,
-    'label_text_font_size': "14pt",
-    'title.text_font_size': "16pt",
-    'subtitle.text_font_size': "14pt",
-    'axis.axis_label_text_font_size': "16pt",
-    'axis.axis_label_text_font_style': "normal",
-    'axis.major_label_text_font_size': "14pt"
-    }
-    plot_dir = root_plot_dir + "variant_qc/" + args.runhash + "/"
-    if not os.path.exists(plot_dir):
-        os.makedirs(plot_dir)
-
-    bin_htfile = rf_dir + args.runhash + "/_rf_result_ranked_BINS.ht"
+    config = parse_config()
+    rf_dir = path_spark(config['general']['var_qc_rf_dir']) # TODO: add adapters inside the functions to enhance robustness
+    root_plot_dir = config['general']['plots_dir']
+
+    # TODO DEBUG: test if this way works
+    qc_plots_settings = config['step3']['create_plots']['qc_plots_settings']
+
+    # qc_plots_settings = {
+    # 'mean_point_size': 4.0,
+    # 'min_point_size': 1.0,
+    # 'max_point_size': 16.0,
+    # 'label_text_font_size': "14pt",
+    # 'title_text_font_size': "16pt",
+    # 'subtitle_text_font_size': "14pt",
+    # 'axis_axis_label_text_font_size': "16pt",
+    # 'axis_axis_label_text_font_style': "normal",
+    # 'axis_major_label_text_font_size': "14pt"
+    # }
+
+    plot_dir = os.path.join(root_plot_dir, "variant_qc", args.runhash)
+    os.makedirs(plot_dir, exist_ok=True) # create if doesn't exist
+
+    bin_htfile = os.path.join(rf_dir, args.runhash, "_rf_result_ranked_BINS.ht")
     create_plots(bin_htfile, plot_dir, args.runhash, qc_plots_settings)
 
 
diff --git a/4-genotype_qc/1-apply_hard_filters.py b/4-genotype_qc/1-apply_hard_filters.py
index 0f67922..1eab49c 100755
--- a/4-genotype_qc/1-apply_hard_filters.py
+++ b/4-genotype_qc/1-apply_hard_filters.py
@@ -2,7 +2,7 @@
 import hail as hl
 import pyspark
 import argparse
-from utils.utils import parse_config
+from utils.utils import parse_config, path_spark, path_local
 
 def get_options():
     '''
@@ -29,7 +29,7 @@ def filter_mt(mtfile: str, dp: int, gq: int, ab: float, mtfile_filtered: str):
     :param float ab: Minimum allele balance for hets
     :param str mtfile_filtered: Output mtfile
     '''
-    mt = hl.read_matrix_table(mtfile)
+    mt = hl.read_matrix_table(path_spark(mtfile))
     prev_count = mt.entries().count()
     var_count = mt.count_rows()
 
@@ -55,7 +55,7 @@ def filter_mt(mtfile: str, dp: int, gq: int, ab: float, mtfile_filtered: str):
     new_count = mt.entries().count()
     new_var_count = mt.count_rows()
 
-    mt.write(mtfile_filtered, overwrite = True)
+    mt.write(path_spark(mtfile_filtered), overwrite = True)
     print(str(prev_count) + " entries prior to filtering, " + str(new_count) + " entries after filtering")
     print(str(var_count) + " variants prior to filtering, " + str(new_var_count) + " variants after filtering")
 
@@ -63,17 +63,17 @@ def filter_mt(mtfile: str, dp: int, gq: int, ab: float, mtfile_filtered: str):
 def main():
     #set up
     args = get_options()
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
-    mtfile = mtdir + "mt_after_var_qc.mt"
-    mtfile_filtered = mtdir + "mt_after_var_qc_hard_filter_gt.mt"
+    mtfile = config['step4']['filter_mt']['mtfile']
+    mtfile_filtered = config['step4']['filter_mt']['mtoutfile_filtered']
     filter_mt(mtfile, args.dp, args.gq, args.ab, mtfile_filtered)
 
 
diff --git a/4-genotype_qc/1a-apply_range_of_hard_filters.py b/4-genotype_qc/1a-apply_range_of_hard_filters.py
index d1fe13b..4958491 100755
--- a/4-genotype_qc/1a-apply_range_of_hard_filters.py
+++ b/4-genotype_qc/1a-apply_range_of_hard_filters.py
@@ -3,7 +3,8 @@
 import hail as hl
 import pyspark
 import argparse
-from utils.utils import parse_config
+import os.path
+from utils.utils import parse_config, path_spark, path_local
 
 
 def get_options():
@@ -27,7 +28,7 @@ def remove_samples(mt: hl.MatrixTable, exclude_file: str):
     :param str exclude_file: path of file with samples to exclude
     :return: hl.MatrixTable
     '''
-    excl_ht = hl.import_table(exclude_file, impute=True, key = 'exomeID')
+    excl_ht = hl.import_table(path_spark(exclude_file), impute=True, key = 'exomeID')
     mt = mt.filter_cols(hl.is_defined(excl_ht[mt.s]), keep=False)
 
     return mt
@@ -42,7 +43,7 @@ def annotate_cq_rf(mt: hl.MatrixTable, rf_htfile: str, cqfile: str) -> hl.Matrix
     :param str cqfile: consequence file
     :return hl.matrixTable:
     '''
-    rf_ht = hl.read_table(rf_htfile)
+    rf_ht = hl.read_table(path_spark(rf_htfile))
     # keep only vars with rank_id = rank
     rf_ht = rf_ht.filter(rf_ht.rank_id == 'rank')
     # annotate mt with score and bin
@@ -55,8 +56,10 @@ def annotate_cq_rf(mt: hl.MatrixTable, rf_htfile: str, cqfile: str) -> hl.Matrix
             rf_bin=rf_ht[mt.row_key].bin)
     )
 
-    cq_ht = hl.import_table(cqfile, types={'f0': 'str', 'f1': 'int32', 'f2': 'str',
-                            'f3': 'str', 'f4': 'str', 'f5': 'str', 'f6': 'str', 'f7': 'str', 'f8': 'str'}, no_header=True)
+    cq_ht = hl.import_table(path_spark(cqfile), 
+                            types={'f0': 'str', 'f1': 'int32', 'f2': 'str',
+                            'f3': 'str', 'f4': 'str', 'f5': 'str', 'f6': 'str', 'f7': 'str', 'f8': 'str'}, 
+                            no_header=True)
     cq_ht = cq_ht.annotate(chr=cq_ht.f0)
     cq_ht = cq_ht.annotate(pos=cq_ht.f1)
     cq_ht = cq_ht.annotate(rs=cq_ht.f2)
@@ -220,7 +223,8 @@ def apply_hard_filters(mt: hl.MatrixTable, hard_filters: dict) -> hl.MatrixTable
     return mt
 
 
-def apply_missingness(mt: hl.MatrixTable, call_rate_stringent: float, call_rate_medium: float, call_rate_relaxed: float) -> hl.MatrixTable:
+def apply_missingness(mt: hl.MatrixTable, call_rate_stringent: float, 
+                      call_rate_medium: float, call_rate_relaxed: float) -> hl.MatrixTable:
     n = mt.count_cols()
 
     mt = mt.annotate_rows(
@@ -243,26 +247,29 @@ def apply_missingness(mt: hl.MatrixTable, call_rate_stringent: float, call_rate_
 def main():
     #set up
     args = get_options()
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
-    rf_dir = inputs['var_qc_rf_dir']
-    resourcedir = inputs['resource_dir']
-    hard_filters = inputs['hard_filters']
-    annotdir = inputs['annotation_lustre_dir']
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
+    rf_dir = path_spark(config['general']['var_qc_rf_dir']) # TODO: use adapters inside the functions to enhance robustness
+    resourcedir = config['general']['resource_dir']
+    annotdir = config['general']['annotation_dir']
+
+
+    hard_filters = config['step4']['apply_hard_filters']['hard_filters']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
+
+    # exclude_file = annotdir + "to_be_excluded_exome.txt" # not used
 
-    exclude_file = annotdir + "to_be_excluded_exome.txt"
-    rf_htfile = rf_dir + args.runhash + "/_gnomad_score_binning_tmp.ht"
-    mtfile = mtdir + "mt_varqc_splitmulti.mt"
-    cqfile = resourcedir + "all_consequences_with_gene_and_csq.txt"
-    mtfile_annot = mtdir + "mt_hard_filter_combinations.mt"
+    rf_htfile = os.path.join(rf_dir, args.runhash, "_gnomad_score_binning_tmp.ht")  # move runhash to config
+    mtfile = config['step4']['annotate_cq_rf']['mtfile']
+    cqfile = config['step4']['annotate_cq_rf']['cqfile'] 
+    mtfile_annot = config['step4']['mtoutfile_annot']
 
-    mt = hl.read_matrix_table(mtfile)
+    mt = hl.read_matrix_table(path_spark(mtfile))
 
     #remove unwanted samples
     # mt = remove_samples(mt, exclude_file)
@@ -272,7 +279,7 @@ def main():
 
     #annotate with all combinations of filters (pass/fail) and add missingness
     mt_annot = apply_hard_filters(mt_annot, hard_filters)
-    mt_annot.write(mtfile_annot, overwrite = True)
+    mt_annot.write(path_spark(mtfile_annot), overwrite = True)
 
 
 if __name__ == '__main__':
diff --git a/4-genotype_qc/2-counts_per_sample.py b/4-genotype_qc/2-counts_per_sample.py
index 2ea95c3..fb30579 100755
--- a/4-genotype_qc/2-counts_per_sample.py
+++ b/4-genotype_qc/2-counts_per_sample.py
@@ -6,7 +6,7 @@
 import pandas as pd
 import numpy as np
 import os
-from wes_qc.utils.utils import parse_config
+from utils.utils import parse_config, path_spark, path_local
 
 
 def annotate_gnomad(mt_in: hl.MatrixTable, gnomad_htfile: str) -> hl.MatrixTable:
@@ -16,7 +16,7 @@ def annotate_gnomad(mt_in: hl.MatrixTable, gnomad_htfile: str) -> hl.MatrixTable
     :param str gnomad_htfile: gnomAD Hail table file
     :return: Annotated MatrixTable
     '''
-    gnomad_ht = hl.read_table(gnomad_htfile)
+    gnomad_ht = hl.read_table(path_spark(gnomad_htfile))
     #ac = gnomadht.freq[0].AC
     #af = gnomadht.freq[0].AF
     mt_in = mt_in.annotate_rows(gnomad_AF=gnomad_ht[mt_in.row_key].freq[0].AF)
@@ -31,9 +31,9 @@ def get_trans_untrans_synon_singleton_counts(mt_in: hl.MatrixTable, pedfile: str
     :param hl.MatrixTable mt_in: Input MatrixTable
     :param str pedfile: Path to pedfile
     '''
-    pedigree = hl.Pedigree.read(pedfile)
+    pedigree = hl.Pedigree.read(path_spark(pedfile))
     # get trios only then filter to trioAC == 1 or 2
-    trio_sample_ht = hl.import_fam(pedfile)
+    trio_sample_ht = hl.import_fam(path_spark(pedfile))
     sample_list = trio_sample_ht.id.collect() + trio_sample_ht.pat_id.collect() + trio_sample_ht.mat_id.collect()
     mt2 = mt_in.filter_cols(hl.set(sample_list).contains(mt_in.s))
     mt2 = hl.variant_qc(mt2, name='varqc_trios')
@@ -105,7 +105,7 @@ def get_counts_per_cq(mt_in: hl.MatrixTable, outfile: str):
 
     n_rows = len(synonymous_all)
     n_cols = len(header)
-    with open(outfile, 'w') as o:
+    with open(path_local(outfile), 'w') as o:
         o.write(("\t").join(header))
         o.write("\n")
         for i in range(0, n_rows):
@@ -125,7 +125,7 @@ def median_count_for_cq(mt_in: hl.MatrixTable, cqs: list) -> tuple:
     '''
 
     mt = mt_in.filter_rows(hl.literal(cqs).contains(mt_in.info.consequence))
-    mt_rare = mt.filter_rows(mt.gnomad_AC < 5)
+    mt_rare = mt.filter_rows(mt.gnomad_AC < 5) # TODO: should be in the config?
 
     mt = hl.sample_qc(mt)
     mt_rare = hl.sample_qc(mt_rare)
@@ -145,7 +145,7 @@ def counts_per_cq(mt_in: hl.MatrixTable, cqs: list) -> tuple:
     :return: dict
     '''
     mt = mt_in.filter_rows(hl.literal(cqs).contains(mt_in.info.consequence))
-    mt_rare = mt.filter_rows(mt.gnomad_AC < 5)
+    mt_rare = mt.filter_rows(mt.gnomad_AC < 5) # TODO: move to config?
     mt = hl.sample_qc(mt)
     mt_rare = hl.sample_qc(mt_rare)
     sampleqc_ht = mt.cols()
@@ -153,12 +153,13 @@ def counts_per_cq(mt_in: hl.MatrixTable, cqs: list) -> tuple:
     counts_all = sampleqc_ht.sample_qc.n_non_ref.collect()
     counts_rare = sampleqc_rare_ht.sample_qc.n_non_ref.collect()
 
-    #remove aggregate intermediates from tmp - this is a hack as this dir fills up and causes this to exit
-    aggdir = "/lustre/scratch123/qc/tmp/aggregate_intermediates/"
-    aggfiles = os.listdir(aggdir)
-    for af in aggfiles:
-        aggpath = aggdir + af
-        os.remove(aggpath)
+    # TODO: refactor this
+    # #remove aggregate intermediates from tmp - this is a hack as this dir fills up and causes this to exit
+    # aggdir = "/lustre/scratch123/qc/tmp/aggregate_intermediates/"
+    # aggfiles = os.listdir(aggdir)
+    # for af in aggfiles:
+    #     aggpath = aggdir + af
+    #     os.remove(aggpath)
 
     return counts_all, counts_rare
 
@@ -171,7 +172,7 @@ def get_ca_fractions(mt_in: hl.MatrixTable, outfile: str):
     '''
     # filter to SNVs and to rare
     snv_mt = mt_in.filter_rows(hl.is_snp(mt_in.alleles[0], mt_in.alleles[1]))
-    snv_mt_rare = snv_mt.filter_rows(snv_mt.gnomad_AC < 5)
+    snv_mt_rare = snv_mt.filter_rows(snv_mt.gnomad_AC < 5) # TODO: to config?
 
     # total_ca_frac = get_median_ca_per_sample(snv_mt)
     # rare_ca_frac = get_median_ca_per_sample(snv_mt_rare)
@@ -186,7 +187,7 @@ def get_ca_fractions(mt_in: hl.MatrixTable, outfile: str):
     n_rows = len(outdata)
     n_cols = len(header)
 
-    with open(outfile, 'w') as o:
+    with open(path_local(outfile), 'w') as o:
         o.write(("\t").join(header))
         o.write("\n")
         for i in range(0, n_rows):
@@ -211,12 +212,13 @@ def get_ca_per_sample(mt_in: hl.MatrixTable) -> list:
     mt_in = hl.sample_qc(mt_in)
     ca_mt = hl.sample_qc(ca_mt)
 
-    #remove aggregate intermediates from tmp - this is a hack as this dir fills up and causes this to exit
-    aggdir = "/lustre/scratch123/qc/tmp/aggregate_intermediates/"
-    aggfiles = os.listdir(aggdir)
-    for af in aggfiles:
-        aggpath = aggdir + af
-        os.remove(aggpath)
+    # TODO: refactor this
+    # #remove aggregate intermediates from tmp - this is a hack as this dir fills up and causes this to exit
+    # aggdir = "/lustre/scratch123/qc/tmp/aggregate_intermediates/"
+    # aggfiles = os.listdir(aggdir)
+    # for af in aggfiles:
+    #     aggpath = aggdir + af
+    #     os.remove(aggpath)
 
     snv_qc = mt_in.cols()
     ca_qc = ca_mt.cols()
@@ -274,29 +276,28 @@ def get_median_ca_per_sample(mt_in: hl.MatrixTable) -> float:
 
 def main():
     # set up
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
-    resourcedir = inputs['resource_dir']
-    plot_dir = inputs['plots_dir_local']
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
+    resourcedir = config['general']['resource_dir']
+    plot_dir = config['general']['plots_dir']
 
     # initialise hail
-    #tmp_dir = "hdfs://spark-master:9820/"
-    tmp_dir = "file:///lustre/scratch123/qc/tmp"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
-
-    mtfile = mtdir + "mt_after_var_qc_hard_filter_gt.mt"
-    gnomad_htfile = resourcedir + "gnomad.exomes.r2.1.1.sites.liftover_grch38.ht"
-    mt = hl.read_matrix_table(mtfile)
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
+    mtfile = config['step4']['annotate_gnomad']['mtfile']
+    gnomad_htfile = config['step4']['annotate_gnomad']['gnomad_htfile']
+    mt = hl.read_matrix_table(path_spark(mtfile))
     mt = annotate_gnomad(mt, gnomad_htfile)
 
-    pedfile = resourcedir + "trios.ped"
-    get_trans_untrans_synon_singleton_counts(mt, pedfile)
+    # TODO: make optional as it only prints info to stdout
+    pedfile = config['step4']['get_trans_untrans_synon_singleton_counts']['pedfile']
+    # get_trans_untrans_synon_singleton_counts(mt, pedfile) # test data has no trios
 
-    cqfile = plot_dir + "/variant_counts_per_cq_post_qc.txt"
-    cafile = plot_dir + "/frac_ca_per_sample_post_qc_snv.txt"
+    cqfile = config['step4']['get_counts_per_cq']['cqfile']
+    cafile = config['step4']['get_ca_fractions']['cafile']
 
     get_counts_per_cq(mt, cqfile)
     get_ca_fractions(mt, cafile)
diff --git a/4-genotype_qc/3-export_vcfs.py b/4-genotype_qc/3-export_vcfs.py
index 7aba19e..ca6fc73 100755
--- a/4-genotype_qc/3-export_vcfs.py
+++ b/4-genotype_qc/3-export_vcfs.py
@@ -2,7 +2,7 @@
 #TODO fix header. decide what fields are needed in the VCF
 import hail as hl
 import pyspark
-from wes_qc.utils.utils import parse_config
+from utils.utils import parse_config, path_spark, path_local
 
 
 def export_vcfs(mtfile: str, vcf_dir: str):
@@ -24,32 +24,32 @@ def export_vcfs(mtfile: str, vcf_dir: str):
                 }
     }
 
-    mt = hl.read_matrix_table(mtfile)
+    mt = hl.read_matrix_table(path_spark(mtfile))
     #drop boolean format field adj
     mt = mt.drop(mt.adj)
 
-    chroms=[*range(1,23),"X","Y"]
+    chroms=[*range(1,23), "X", "Y"]
     chromosomes=["chr"+ str(chr) for chr in chroms]
     for chromosome in chromosomes:
         print("Exporting " + chromosome)
-        mt_chrom=mt.filter_rows(mt.locus.contig==chromosome)
+        mt_chrom = mt.filter_rows(mt.locus.contig==chromosome)
         outfile = vcf_dir + chromosome + "_filtered.vcf.bgz"
         hl.export_vcf(mt_chrom, outfile, metadata = metadata)
 
 
 def main():
     #set up
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
-    filtered_vcf_dir = inputs['vcf_output_dir']
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
-    mtfile_filtered = mtdir + "mt_after_var_qc_hard_filter_gt.mt"
+    filtered_vcf_dir = config['step4']['export_vcfs']['vcf_output_dir']
+    mtfile_filtered = config['step4']['export_vcfs']['mtfile_filtered']
     export_vcfs(mtfile_filtered, filtered_vcf_dir)
 
 
diff --git a/4-genotype_qc/3a-export_vcfs_range_of_hard_filters.py b/4-genotype_qc/3a-export_vcfs_range_of_hard_filters.py
index a936d14..73cfab9 100755
--- a/4-genotype_qc/3a-export_vcfs_range_of_hard_filters.py
+++ b/4-genotype_qc/3a-export_vcfs_range_of_hard_filters.py
@@ -3,8 +3,9 @@
 import hail as hl
 import pyspark
 import argparse
-from utils.utils import parse_config
+from utils.utils import parse_config, path_spark, path_local
 
+# TODO move to utils constants
 fail_string = 'FAIL'
 outside_bait_string = 'OUTSIDE_BAIT'
 pass_medium_string = 'PASS_MEDIUM'
@@ -16,7 +17,7 @@ def get_options():
     Get options from the command line
     '''
     parser = argparse.ArgumentParser()
-    parser.add_argument("--runhash", help="RF run hash")
+    parser.add_argument("--runhash", help="RF run hash") # TODO: set in config
     args = parser.parse_args()
     if not args.runhash:
         print("--runhash must be specified")
@@ -33,7 +34,7 @@ def export_vcfs(mtfile: str, filtered_vcf_dir: str, hard_filters: dict, run_hash
     :param dict hard_filters: details of all sets of filters
     :param str run_hash: random forest run hash used
     '''
-    mt = hl.read_matrix_table(mtfile)
+    mt = hl.read_matrix_table(path_spark(mtfile))
 
     # filter to remove rows where all variants fail the most relaxed filters
     mt = mt.filter_rows(mt.info.fraction_pass_relaxed_filters > 0)
@@ -165,25 +166,27 @@ def export_vcfs(mtfile: str, filtered_vcf_dir: str, hard_filters: dict, run_hash
         print("Exporting " + chromosome)
         mt_chrom = mt.annotate_globals(chromosome=chromosome)
         mt_chrom = mt_chrom.filter_rows(mt_chrom.locus.contig == mt_chrom.chromosome)
-        outfile = os.path.join(filtered_vcf_dir,  f"{chromosome}_hard_filters.vcf.bgz")
+        outfile = os.path.join(path_spark(filtered_vcf_dir),  f"{chromosome}_hard_filters.vcf.bgz")
         hl.export_vcf(mt_chrom, outfile, metadata=metadata)
 
 
 def main():
     # set up
-    inputs = parse_config()
     args = get_options()
-    mtdir = inputs['matrixtables_lustre_dir']
-    hard_filters = inputs['hard_filters']
-    filtered_vcf_dir = inputs['vcf_output_dir']
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
+    hard_filters = config['step4']['apply_hard_filters']['hard_filters'] # set in step 4.1a
+
+    
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
-    mtfile = mtdir + "mt_hard_filter_combinations.mt"
+    mtfile = config['step4']['export_vcfs_a']['mtfile']
+    filtered_vcf_dir = config['step4']['export_vcfs_a']['vcf_output_dir']
     export_vcfs(mtfile, filtered_vcf_dir, hard_filters, args.runhash)
 
 
diff --git a/4-genotype_qc/3b-export_vcfs_stingent_filters.py b/4-genotype_qc/3b-export_vcfs_stingent_filters.py
index afddeb1..669a3f8 100755
--- a/4-genotype_qc/3b-export_vcfs_stingent_filters.py
+++ b/4-genotype_qc/3b-export_vcfs_stingent_filters.py
@@ -3,7 +3,7 @@
 import pyspark
 import argparse
 import os.path
-from utils.utils import parse_config
+from utils.utils import parse_config, path_spark, path_local
 
 
 def get_options():
@@ -28,7 +28,7 @@ def export_vcfs(mtfile: str, filtered_vcf_dir: str, hard_filters: dict, run_hash
     :param dict hard_filters: details of all sets of filters
     :param str run_hash: random forest run hash used
     '''
-    mt = hl.read_matrix_table(mtfile)
+    mt = hl.read_matrix_table(path_spark(mtfile))
     # remove control samples
     samples_to_exclude = ['EGAN00003332049', 'EGAN00003332050', 'EGAN00003332051', 'EGAN00003332052', 
                           'EGAN00003332053', 'EGAN00003332049_remapped', 'EGAN00003332050_remapped', 
@@ -90,32 +90,32 @@ def export_vcfs(mtfile: str, filtered_vcf_dir: str, hard_filters: dict, run_hash
         }
     }
 
-    #export per chromosome
-    chroms=[*range(1,23),"X","Y"]
-    chromosomes=["chr"+ str(chr) for chr in chroms]
+    # export per chromosome
+    chroms = [*range(1, 23), "X", "Y"]
+    chromosomes=[f'chr{str(chr)}' for chr in chroms]
     for chromosome in chromosomes:
         print("Exporting " + chromosome)
         mt_chrom = mt.annotate_globals(chromosome=chromosome)
         mt_chrom = mt_chrom.filter_rows(mt_chrom.locus.contig == mt_chrom.chromosome)
-        outfile = os.path.join(filtered_vcf_dir,  f"{chromosome}_stringent_filters.vcf.bgz")
+        outfile = os.path.join(path_spark(filtered_vcf_dir),  f"{chromosome}_stringent_filters.vcf.bgz")
         hl.export_vcf(mt_chrom, outfile, metadata = metadata)
 
 
 def main():
     # set up
-    inputs = parse_config()
     args = get_options()
-    mtdir = inputs['matrixtables_lustre_dir']
-    hard_filters = inputs['hard_filters']
-    filtered_vcf_dir = 'file:///lustre/scratch123/qc/BiB/filtered_vcfs_stringent/'
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
+    hard_filters = config['step4']['apply_hard_filters']['hard_filters'] # set during step 4.1a
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
-    mtfile = mtdir + "mt_hard_filter_combinations.mt"
+    mtfile = config['step4']['export_vcfs_b']['mtfile']
+    filtered_vcf_dir = config['step4']['export_vcfs_b']['filtered_vcf_dir']
     export_vcfs(mtfile, filtered_vcf_dir, hard_filters, args.runhash)
 
 
diff --git a/config/.inputs.yaml.swp b/config/.inputs.yaml.swp
new file mode 100644
index 0000000..b9bf56c
Binary files /dev/null and b/config/.inputs.yaml.swp differ
diff --git a/config/inputs-mk43-a.yaml b/config/inputs-mk43-a.yaml
new file mode 100644
index 0000000..fe6e126
--- /dev/null
+++ b/config/inputs-mk43-a.yaml
@@ -0,0 +1,205 @@
+---
+
+# - You can insert a variable in the string value via '{}'. For example, 
+#   'foo {var_name} baz' with `var_name: bar` will render to 'foo bar baz'. 
+#
+# - If a config field ends with 'dir' or 'file', then parser will consider 
+#   this field as a path and normalize it, thus removing double slashes (foo//bar -> foo/bar)
+#   and redundand dots (foo/./bar -> foo/bar).
+#
+# - Note that string quotes are MANDATORY if using cvars.
+#   That is, variable should be used only inside an explicit string.
+#   Curly braces outside a string will break the YAML parser.
+#
+# - You can use dot-separated name of any config field as a variable name like this:
+#   a:
+#     a1: bar
+#     a2: baz
+#   b: 'foo {a.a1} {a.a2}' (will render to 'foo bar baz')
+#
+# - Special variables from 'cvars' list will be replaced with field  
+#   they are referring to. For example, '{mtdir}/gatk_unprocessed.mt' is 
+#   equivalent to '{general.matrixtables_dir}/gatk_unprocessed.mt'
+#
+# - Parser can only insert variables that were already defined. 
+#   You can't use a variable that will be defined further down the config.
+
+# TODO: custom yaml type for paths
+# TODO: ensure strict variable substitution, from top to bottom of the config
+# TODO: add testcases for cvars, for order of variables, for nested variables  
+cvars:
+  tmpdir: general.tmp_dir
+  anndir: general.annotation_dir
+  mtdir: general.matrixtables_dir
+  resdir: general.resource_dir
+  pltdir: general.plots_dir
+
+general:
+  # CVAR tmpdir
+  tmp_dir: /lustre/scratch126/mk43/tmp/
+  # tmp_dir: hdfs://spark-master:9820/
+
+  # CVAR anndir
+  annotation_dir: /lustre/scratch126/dh24_test/qc_test/BiB/annotations/
+  
+  # CVAR mtdir
+  matrixtables_dir: /lustre/scratch126/dh24_test/qc_test/BiB/matrixtables/
+
+  # TODO: document resource_dir
+  # TODO: add option to override in `resources` config field
+  # TODO: add Jira ticket
+  # CVAR resdir
+  resource_dir: /lustre/scratch126/dh24_test/qc_test/BiB/resources/
+
+  # CVAR pltdir
+  plots_dir: /lustre/scratch126/dh24_test/qc_test/BiB/plots/
+
+# --- Step 1.1 --- #
+step1:
+  gatk_vcf_header_infile:
+  gatk_vcf_indir: /lustre/scratch126/WES_QC/control_set_vcfs/control_set_small/
+  gatk_mt_outfile: '{mtdir}/gatk_unprocessed.mt'
+
+step2:
+  # --- Step 2.1 --- #
+  sex_annotation_hard_filters:
+    filtered_mt_outfile: '{mtdir}/mt_hard_filters_annotated.mt'
+    n_alt_alleles_threshold: 0.001
+    defined_gt_frac_threshold: 0.99
+
+  impute_sex:
+    sex_ht_outfile: '{anndir}/sex_annotated.sex_check.txt.bgz'
+    sex_mt_outfile: '{mtdir}/mt_sex_annotated.mt'
+    female_threshold: 0.5
+    male_threshold: 0.8
+    aaf_threshold: 0.05
+    
+  sex_inconsistencies:
+    # TODO: specify structure of a sex metadata file
+    sex_metadata_file: '{resdir}/mlwh_sample_and_sex.txt'
+    conflicting_sex_report_file: '{anndir}/conflicting_sex.txt.bgz'
+    fstat_outliers_report_file: '{anndir}/sex_annotation_f_stat_outliers.txt.bgz'
+    fstat_low: 0.2
+    fstat_high: 0.8
+
+  # --- Step 2.2 --- #
+  prune:
+    pruned_mt_file: '{mtdir}/mt_ldpruned.mt'
+    ld_prune_args:
+      r2: 0.2
+      # bp_window_size:
+      # memory_per_core:
+      # keep_higher_maf:
+      # block_size: 
+
+  # preciously pc_relate
+  prune_pc_relate:
+    relatedness_ht_file: '{mtdir}/mt_relatedness.ht'
+    samples_to_remove_file: '{mtdir}/mt_related_samples_to_remove.ht'
+    scores_file: '{mtdir}/mt_pruned.pca_scores.ht'
+    pca_components: 3
+    pc_relate_args:
+      min_individual_maf: 0.05
+      block_size: 4096
+      min_kinship: 0.05
+      statistics: 'kin2'
+      # k:
+      # include_self_kinship:
+    relatedness_column: 'kin'
+    relatedness_threshold: 0.125
+    
+  # previously population_pca
+  prune_plot_pca:
+    plink_outfile: '{mtdir}/mt_unrelated.plink'
+
+    pca_components: 4
+    pca_scores_file: '{mtdir}/mt_pca_scores.ht'
+    pca_loadings_file: '{mtdir}/mt_pca_loadings.ht'
+    pca_mt_file: '{mtdir}/mt_pca.mt'
+
+    plot_outfile: '{pltdir}/pca.html'
+
+  # --- Step 2.3 --- #
+  # tmp before dh's merge
+  pop_pred_pca:
+    pca_scores_file: '{mtdir}/pca_scores_after_pruning.ht'
+    pca_loadings_file: '{mtdir}/pca_loadings_after_pruning.ht'
+    pca_evals_file: '{mtdir}/pca_evals_after_pruning.txt'
+
+  predict_populations:
+    pop_ht_file: '{mtdir}/pop_assignments.ht'
+    pop_ht_tsv: '{mtdir}/pop_assignments.tsv'
+
+  # --- Step 2.4 --- #
+
+  # annotate_mt
+  annotate_with_pop:
+    annotated_mt_file: '{mtdir}/gatk_unprocessed_with_pop.mt'
+
+  stratified_sample_qc:
+    mt_qc_outfile: '{mtdir}/mt_pops_sampleqc.mt'
+    ht_qc_cols_outfile: '{mtdir}/mt_pops_sampleqc.ht'
+    qc_filter_file: '{mtdir}/mt_pops_QC_filters.ht'
+
+    min_depth: 20
+    min_genotype_quality: 20
+    min_vaf: 0.25
+    output_text_file: '{anndir}/sample_qc_by_pop.tsv.bgz'
+    output_globals_json_file: '{anndir}/sample_qc_by_pop.globals.json'
+  
+  # --- Step 2.5 --- #
+
+  remove_sample_qc_fails:
+    samples_failing_qc_file: '{anndir}/samples_failing_qc.tsv.bgz'
+    sample_qc_filtered_mt_file: '{mtdir}/mt_pops_QC_filters_after_sample_qc.mt'
+
+# unprocessed below this line
+
+plots_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/plots/
+plots_dir_local: /lustre/scratch126/dh24_test/qc_test/BiB/plots/
+
+training_set_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/training_sets/
+var_qc_rf_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/variant_qc_random_forest/
+vcf_output_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/filtered_vcfs/
+
+# TODO: this is a redundant field that differs to matrixtables_dir only in prefix
+load_matrixtables_lustre_dir: /lustre/scratch126/dh24_test/qc_test/BiB/matrixtables/
+
+
+rf_test_interval: chr20
+
+#hard filter
+hard_filters:
+  missingness: 0.5
+  snp:
+    relaxed:
+      bin: 92
+      dp: 5
+      gq: 10
+      ab: 0.2
+    medium:
+      bin: 88
+      dp: 5
+      gq: 10
+      ab: 0.2
+    stringent:
+      bin: 84
+      dp: 5
+      gq: 15
+      ab: 0.2
+  indel:
+    relaxed:
+      bin: 68
+      dp: 5
+      gq: 10
+      ab: 0.2
+    medium:
+      bin: 66
+      dp: 5
+      gq: 15
+      ab: 0.2
+    stringent:
+      bin: 58
+      dp: 5
+      gq: 20
+      ab: 0.3
diff --git a/config/inputs.yaml b/config/inputs.yaml
index 91bbbd2..8d58258 100644
--- a/config/inputs.yaml
+++ b/config/inputs.yaml
@@ -1,19 +1,30 @@
 ---
-gatk_vcf_header: file:///lustre/scratch123/qc/BiB/gatk_vcf_header.txt
-gatk_import_lustre_dir: file:///lustre/scratch123/qc/BiB/gatk_vcfs/
-load_matrixtables_lustre_dir: /lustre/scratch123/qc/BiB/matrixtables/
-#load_matrixtables_lustre_dir: /lustre/scratch123/qc/matrixtables/mts_for_control_datasets/
-annotation_lustre_dir: file:///lustre/scratch123/qc/BiB/annotations/
-annotation_lustre_dir_local: /lustre/scratch123/qc/BiB/annotations/
-matrixtables_lustre_dir: file:///lustre/scratch123/qc/BiB/matrixtables/
-#matrixtables_lustre_dir: file:///lustre/scratch123/qc/matrixtables/mts_for_control_datasets/
-plots_lustre_dir: file:///lustre/scratch123/qc/BiB/plots/
-plots_dir_local: /lustre/scratch123/qc/BiB/plots/
-resource_dir: file:///lustre/scratch123/qc/BiB/resources/
-resource_dir_local: /lustre/scratch123/qc/BiB/resources/
-training_set_dir: file:///lustre/scratch123/qc/BiB/training_sets/
-var_qc_rf_dir: file:///lustre/scratch123/qc/BiB/variant_qc_random_forest/
-vcf_output_dir: file:///lustre/scratch123/qc/BiB/filtered_vcfs/
+
+# hail setup parameter
+tmp_dir: file:///lustre/scratch126/dh24_test/tmp
+
+# --- Step 1.1 --- #
+gatk_vcf_header: file:///lustre/scratch126/dh24_test/qc_test/BiB/gatk_vcf_header.txt # TODO: make optional
+gatk_import_lustre_dir: file:///lustre/scratch126/dh24_test/control_set_small # test with the small dataset
+load_matrixtables_lustre_dir: /lustre/scratch126/dh24_test/qc_test/BiB/matrixtables/ # not used in this step
+# matrixtables_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/matrixtables/ # used in this step 
+
+# --- Step 2.1 --- #
+#load_matrixtables_lustre_dir: /lustre/scratch126/dh24_test/qc_test/matrixtables/mts_for_control_datasets/
+annotation_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/annotations/
+annotation_lustre_dir_local: /lustre/scratch126/dh24_test/qc_test/BiB/annotations/ # TODO: clarify the purpose of these _local duplicates, not used in this step
+matrixtables_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/matrixtables/
+resource_dir: file:///lustre/scratch126/dh24_test/resources/
+
+# --- Step 2.2 --- #
+#matrixtables_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/matrixtables/mts_for_control_datasets/
+plots_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/plots/ # TODO: not used?
+plots_dir_local: /lustre/scratch126/dh24_test/qc_test/BiB/plots/
+# resource_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/resources/
+resource_dir_local: /lustre/scratch126/dh24_test/qc_test/BiB/resources/
+training_set_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/training_sets/
+var_qc_rf_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/variant_qc_random_forest/
+vcf_output_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/filtered_vcfs/
 
 rf_test_interval: chr20
 
diff --git a/config/inputs_1000G_small.yaml b/config/inputs_1000G_small.yaml
new file mode 100644
index 0000000..bed57dd
--- /dev/null
+++ b/config/inputs_1000G_small.yaml
@@ -0,0 +1,69 @@
+---
+
+# === control_set_1000G === # 
+
+# WARNING: this test dataset is already QC'ed which means that steps 2.4-2.5 won't run #
+
+# hail setup parameter
+tmp_dir: file:///lustre/scratch126/dh24_test/tmp
+
+# --- Step 1.1 --- #
+gatk_vcf_header: file:///lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/gatk_vcf_header.txt # TODO: make optional
+gatk_import_lustre_dir: file:///lustre/scratch126/dh24_test/control_set_from_1000G
+load_matrixtables_lustre_dir: /lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/matrixtables/ # not used in this step
+# matrixtables_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/matrixtables/ # used in this step 
+
+# --- Step 2.1 --- #
+#load_matrixtables_lustre_dir: /lustre/scratch126/dh24_test/qc_test/matrixtables/mts_for_control_datasets/
+annotation_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/annotations/
+annotation_lustre_dir_local: /lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/annotations/ # TODO: clarify the purpose of these _local duplicates, not used in this step
+matrixtables_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/matrixtables/
+resource_dir: file:///lustre/scratch126/dh24_test/resources/
+
+# --- Step 2.2 --- #
+#matrixtables_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/matrixtables/mts_for_control_datasets/
+plots_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/plots/ # TODO: not used?
+plots_dir_local: /lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/plots/
+# resource_dir: file:///lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/resources/
+resource_dir_local: /lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/resources/
+training_set_dir: file:///lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/training_sets/
+var_qc_rf_dir: file:///lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/variant_qc_random_forest/
+vcf_output_dir: file:///lustre/scratch126/dh24_test/qc_test/control_set_from_1000G_qc/filtered_vcfs/
+
+rf_test_interval: chr20
+
+#hard filter
+hard_filters:
+  missingness: 0.5
+  snp:
+    relaxed:
+      bin: 92
+      dp: 5
+      gq: 10
+      ab: 0.2
+    medium:
+      bin: 88
+      dp: 5
+      gq: 10
+      ab: 0.2
+    stringent:
+      bin: 84
+      dp: 5
+      gq: 15
+      ab: 0.2
+  indel:
+    relaxed:
+      bin: 68
+      dp: 5
+      gq: 10
+      ab: 0.2
+    medium:
+      bin: 66
+      dp: 5
+      gq: 15
+      ab: 0.2
+    stringent:
+      bin: 58
+      dp: 5
+      gq: 20
+      ab: 0.3
diff --git a/config/inputs_control_set_small.yaml b/config/inputs_control_set_small.yaml
new file mode 100644
index 0000000..8d58258
--- /dev/null
+++ b/config/inputs_control_set_small.yaml
@@ -0,0 +1,65 @@
+---
+
+# hail setup parameter
+tmp_dir: file:///lustre/scratch126/dh24_test/tmp
+
+# --- Step 1.1 --- #
+gatk_vcf_header: file:///lustre/scratch126/dh24_test/qc_test/BiB/gatk_vcf_header.txt # TODO: make optional
+gatk_import_lustre_dir: file:///lustre/scratch126/dh24_test/control_set_small # test with the small dataset
+load_matrixtables_lustre_dir: /lustre/scratch126/dh24_test/qc_test/BiB/matrixtables/ # not used in this step
+# matrixtables_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/matrixtables/ # used in this step 
+
+# --- Step 2.1 --- #
+#load_matrixtables_lustre_dir: /lustre/scratch126/dh24_test/qc_test/matrixtables/mts_for_control_datasets/
+annotation_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/annotations/
+annotation_lustre_dir_local: /lustre/scratch126/dh24_test/qc_test/BiB/annotations/ # TODO: clarify the purpose of these _local duplicates, not used in this step
+matrixtables_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/matrixtables/
+resource_dir: file:///lustre/scratch126/dh24_test/resources/
+
+# --- Step 2.2 --- #
+#matrixtables_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/matrixtables/mts_for_control_datasets/
+plots_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/plots/ # TODO: not used?
+plots_dir_local: /lustre/scratch126/dh24_test/qc_test/BiB/plots/
+# resource_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/resources/
+resource_dir_local: /lustre/scratch126/dh24_test/qc_test/BiB/resources/
+training_set_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/training_sets/
+var_qc_rf_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/variant_qc_random_forest/
+vcf_output_dir: file:///lustre/scratch126/dh24_test/qc_test/BiB/filtered_vcfs/
+
+rf_test_interval: chr20
+
+#hard filter
+hard_filters:
+  missingness: 0.5
+  snp:
+    relaxed:
+      bin: 92
+      dp: 5
+      gq: 10
+      ab: 0.2
+    medium:
+      bin: 88
+      dp: 5
+      gq: 10
+      ab: 0.2
+    stringent:
+      bin: 84
+      dp: 5
+      gq: 15
+      ab: 0.2
+  indel:
+    relaxed:
+      bin: 68
+      dp: 5
+      gq: 10
+      ab: 0.2
+    medium:
+      bin: 66
+      dp: 5
+      gq: 15
+      ab: 0.2
+    stringent:
+      bin: 58
+      dp: 5
+      gq: 20
+      ab: 0.3
diff --git a/config/inputs_old.yaml b/config/inputs_old.yaml
new file mode 100644
index 0000000..91bbbd2
--- /dev/null
+++ b/config/inputs_old.yaml
@@ -0,0 +1,54 @@
+---
+gatk_vcf_header: file:///lustre/scratch123/qc/BiB/gatk_vcf_header.txt
+gatk_import_lustre_dir: file:///lustre/scratch123/qc/BiB/gatk_vcfs/
+load_matrixtables_lustre_dir: /lustre/scratch123/qc/BiB/matrixtables/
+#load_matrixtables_lustre_dir: /lustre/scratch123/qc/matrixtables/mts_for_control_datasets/
+annotation_lustre_dir: file:///lustre/scratch123/qc/BiB/annotations/
+annotation_lustre_dir_local: /lustre/scratch123/qc/BiB/annotations/
+matrixtables_lustre_dir: file:///lustre/scratch123/qc/BiB/matrixtables/
+#matrixtables_lustre_dir: file:///lustre/scratch123/qc/matrixtables/mts_for_control_datasets/
+plots_lustre_dir: file:///lustre/scratch123/qc/BiB/plots/
+plots_dir_local: /lustre/scratch123/qc/BiB/plots/
+resource_dir: file:///lustre/scratch123/qc/BiB/resources/
+resource_dir_local: /lustre/scratch123/qc/BiB/resources/
+training_set_dir: file:///lustre/scratch123/qc/BiB/training_sets/
+var_qc_rf_dir: file:///lustre/scratch123/qc/BiB/variant_qc_random_forest/
+vcf_output_dir: file:///lustre/scratch123/qc/BiB/filtered_vcfs/
+
+rf_test_interval: chr20
+
+#hard filter
+hard_filters:
+  missingness: 0.5
+  snp:
+    relaxed:
+      bin: 92
+      dp: 5
+      gq: 10
+      ab: 0.2
+    medium:
+      bin: 88
+      dp: 5
+      gq: 10
+      ab: 0.2
+    stringent:
+      bin: 84
+      dp: 5
+      gq: 15
+      ab: 0.2
+  indel:
+    relaxed:
+      bin: 68
+      dp: 5
+      gq: 10
+      ab: 0.2
+    medium:
+      bin: 66
+      dp: 5
+      gq: 15
+      ab: 0.2
+    stringent:
+      bin: 58
+      dp: 5
+      gq: 20
+      ab: 0.3
diff --git a/config/new_config_example.yaml b/config/new_config_example.yaml
new file mode 100644
index 0000000..c352750
--- /dev/null
+++ b/config/new_config_example.yaml
@@ -0,0 +1,393 @@
+---
+
+# - You can insert a variable in the string value via '{}'. For example, 
+#   'foo {var_name} baz' with `var_name: bar` will render to 'foo bar baz'. 
+#
+# - If a config field ends with 'dir' or 'file', then parser will consider 
+#   this field as a path and normalize it, thus removing double slashes (foo//bar -> foo/bar)
+#   and redundand dots (foo/./bar -> foo/bar).
+#
+# - Note that string quotes are MANDATORY if using cvars.
+#   That is, variable should be used only inside an explicit string.
+#   Curly braces outside a string will break the YAML parser.
+#
+# - You can use dot-separated name of any config field as a variable name like this:
+#   a:
+#     a1: bar
+#     a2: baz
+#   b: 'foo {a.a1} {a.a2}' (will render to 'foo bar baz')
+#
+# - Special variables from 'cvars' list will be replaced with field  
+#   they are referring to. For example, '{mtdir}/gatk_unprocessed.mt' is 
+#   equivalent to '{general.matrixtables_dir}/gatk_unprocessed.mt'
+#
+# - Parser can only insert variables that were already defined. 
+#   You can't use a variable that will be defined further down the config.
+
+# TODO: custom yaml type for paths
+# TODO: ensure strict variable substitution, from top to bottom of the config
+# TODO: add testcases for cvars, for order of variables, for nested variables  
+cvars:
+  tmpdir: general.tmp_dir
+  anndir: general.annotation_dir
+  mtdir: general.matrixtables_dir
+  resdir: general.resource_dir
+  1kg_resdir: general.onekg_resource_dir
+  pltdir: general.plots_dir
+  traindir: general.training_sets_dir
+  rfdir: general.var_qc_rf_dir
+
+general:
+  # CVAR tmpdir
+  tmp_dir: /lustre/scratch126/dh24_test/wes-qc/tmp/ # output
+
+  # CVAR anndir
+  annotation_dir: /lustre/scratch126/dh24_test/wes-qc/annotations/ # output
+  
+  # CVAR mtdir
+  matrixtables_dir: /lustre/scratch126/dh24_test/wes-qc/matrixtables/ # output
+
+  # CVAR resdir
+  resource_dir: /lustre/scratch126/dh24_test/wes-qc/tests/resources/ # input and output
+
+  # CVAR 1kg_resdir
+  onekg_resource_dir: /lustre/scratch126/dh24_test/wes-qc/tests/resources/mini_1000G # input; must be without trailing slash (TODO: make more robust)
+
+  # CVAR pltdir
+  plots_dir: /lustre/scratch126/dh24_test/wes-qc/tests/plots/ # output
+
+  # CVAR traindir
+  training_sets_dir: /lustre/scratch126/dh24_test/wes-qc/tests/training_sets/ # input
+
+  # CVAR rfdir
+  var_qc_rf_dir: /lustre/scratch126/dh24_test/wes-qc/tests/variant_qc_random_forest/ # output
+
+
+step1:
+  # --- Step 1.1 --- #
+  gatk_vcf_header_infile:
+  gatk_vcf_indir: /lustre/scratch126/WES_QC/control_set_vcfs/control_set_small/
+  gatk_mt_outfile: '{mtdir}/gatk_unprocessed.mt'
+
+step2:
+  # --- Step 2.1 --- #
+  sex_annotation_hard_filters:
+    filtered_mt_outfile: '{mtdir}/mt_hard_filters_annotated.mt'
+    n_alt_alleles_threshold: 0.001
+    defined_gt_frac_threshold: 0.99
+
+  impute_sex:
+    sex_ht_outfile: '{anndir}/sex_annotated.sex_check.txt.bgz'
+    sex_mt_outfile: '{mtdir}/mt_sex_annotated.mt'
+    female_threshold: 0.5
+    male_threshold: 0.8
+    aaf_threshold: 0.05
+    
+  sex_inconsistencies:
+    # TODO: specify structure of a sex metadata file
+    sex_metadata_file: '{resdir}/mlwh_sample_and_sex.txt'
+    conflicting_sex_report_file: '{anndir}/conflicting_sex.txt.bgz' # output
+    fstat_outliers_report_file: '{anndir}/sex_annotation_f_stat_outliers.txt.bgz' # output
+    fstat_low: 0.2
+    fstat_high: 0.8
+
+  # --- Step 2.2 --- #
+  prune:
+    pruned_mt_file: '{mtdir}/mt_ldpruned.mt' # output
+    ld_prune_args:
+      r2: 0.2
+      # bp_window_size:
+      # memory_per_core:
+      # keep_higher_maf:
+      # block_size: 
+
+  # previously pc_relate
+  prune_pc_relate:
+    relatedness_ht_file: '{mtdir}/mt_relatedness.ht' # output
+    samples_to_remove_file: '{mtdir}/mt_related_samples_to_remove.ht' # output
+    scores_file: '{mtdir}/mt_pruned.pca_scores.ht' # output
+    pca_components: 3
+    pc_relate_args:
+      min_individual_maf: 0.05
+      block_size: 4096
+      min_kinship: 0.05
+      statistics: 'kin2'
+      # k:
+      # include_self_kinship:
+    relatedness_column: 'kin'
+    relatedness_threshold: 0.125
+    
+  # previously population_pca
+  prune_plot_pca:
+    plink_outfile: '{mtdir}/mt_unrelated.plink'
+    pca_components: 4
+    pca_scores_file: '{mtdir}/mt_pca_scores.ht' # output 
+    pca_loadings_file: '{mtdir}/mt_pca_loadings.ht' # output 
+    pca_mt_file: '{mtdir}/mt_pca.mt' # output
+    plot_outfile: '{pltdir}/pca.html' # output
+  
+  # --- Step 2.3 --- #
+  create_1kg_mt:
+    indir: '{1kg_resdir}'
+    vcfheader: '{1kg_resdir}/header_20201028.txt' # not available for the test data, this parameter is ignored
+    mt_out_file: '{mtdir}/kg_wes_regions.mt' # output
+
+  merge_with_1_kg:
+    kg_mt_file: '{mtdir}/kg_wes_regions.mt'
+    merged_mt_outfile: '{mtdir}/merged_with_1kg.mt' # output 
+
+  annotate_and_filter:
+    pops_file: '{resdir}/igsr_samples.tsv'
+    call_rate: 0.99
+    AF: 0.05
+    p_value_hwe: 0.00005
+    long_range_ld_file: '{resdir}/long_ld_regions.hg38.bed'
+    filtered_mt_outfile: '{mtdir}/merged_with_1kg_filtered.mt'
+  
+  run_pca:
+    pca_scores_outfile: '{mtdir}/pca_scores_after_pruning.ht'
+    pca_loadings_outfile: '{mtdir}/pca_loadings_after_pruning.ht'
+    pca_evals_outfile: '{mtdir}/pca_evals_after_pruning.txt' # TODO: don't add prefix
+
+  predict_pops:
+    pca_scores_file: '{mtdir}/pca_scores_after_pruning.ht'
+    gnomad_pc_n_estimators: 100
+    gnomad_prop_train: 0.8
+    gnomad_min_prob: 0.5
+    pop_ht_outfile: '{mtdir}/pop_assignments.ht'
+    pop_ht_outtsv: '{mtdir}/pop_assignments.tsv'
+  
+  # --- Step 2.4 --- #
+  # func name: annotate_mt
+  annotate_with_pop:
+    annotated_mt_file: '{mtdir}/gatk_unprocessed_with_pop.mt' # output
+
+  stratified_sample_qc:
+    mt_qc_outfile: '{mtdir}/mt_pops_sampleqc.mt' # output 
+    ht_qc_cols_outfile: '{mtdir}/mt_pops_sampleqc.ht' # output
+    qc_filter_file: '{mtdir}/mt_pops_QC_filters.ht' # output
+
+    min_depth: 20
+    min_genotype_quality: 20
+    min_vaf: 0.25
+    output_text_file: '{anndir}/sample_qc_by_pop.tsv.bgz' # output
+    output_globals_json_file: '{anndir}/sample_qc_by_pop.globals.json' # output
+  
+  # --- Step 2.5 --- #
+  remove_sample_qc_fails:
+    samples_failing_qc_file: '{anndir}/samples_failing_qc.tsv.bgz' # output
+    sample_qc_filtered_mt_file: '{mtdir}/mt_pops_QC_filters_after_sample_qc.mt' # output
+
+
+step3:
+  # Parameters used in multiple functions # 
+  pedfile: '{resdir}/trios.EGAN.complete.ped'
+
+  # --- Step 3.1 --- #
+  get_truth_ht:
+    truth_ht_outfile: '{resdir}/truthset_table.ht'
+    omni: '{traindir}/1000G_omni2.5.hg38.ht'
+    mills: '{traindir}/Mills_and_1000G_gold_standard.indels.hg38.ht'
+    thousand_genomes: '{traindir}/1000G_phase1.snps.high_confidence.hg38.ht' 
+    hapmap: '{traindir}/hapmap_3.3.hg38.ht'
+
+  split_multi_and_var_qc:
+    mtfile: '{mtdir}/mt_pops_QC_filters_after_sample_qc.mt' # gatk_broad_crams_sanger_calls.mt for non-trios mode
+    varqc_mtoutfile: '{mtdir}/mt_varqc.mt'
+    varqc_mtoutfile_split: '{mtdir}/mt_varqc_splitmulti.mt'
+
+  # not used for non-trios mode
+  trio_family_dnm_annotation:
+    trio_mtoutfile: '{mtdir}/trios.mt'
+    trio_stats_htoutfile: '{mtdir}/trio_stats.ht'
+    fam_stats_htoutfile: '{mtdir}/family_stats.ht'
+    fam_stats_mtoutfile: '{mtdir}/family_stats.mt'
+    fam_stats_gnomad_mtoutfile: '{mtdir}/family_stats_gnomad.mt'
+    gnomad_htfile: '{resdir}/gnomad.exomes.r2.1.1.sites.liftover_grch38.ht'
+    dnm_htoutfile: '{mtdir}/denovo_table.ht'
+
+  create_inbreeding_ht_with_ac_and_allele_data:
+    inbreeding_htoutfile: '{mtdir}/inbreeding.ht'
+    qc_ac_htoutfile: '{mtdir}/qc_ac.ht'
+    allele_data_htoutfile: '{mtdir}/allele_data.ht'
+
+  # --- Step 3.2 --- #
+  create_rf_ht:
+    fail_hard_filters_QD_less_than: 2
+    fail_hard_filters_FS_greater_than: 60
+    fail_hard_filters_MQ_less_than: 30
+
+    truthset_file: '{resdir}/truthset_table.ht'
+    trio_stats_file: '{mtdir}/trio_stats.ht'
+    allele_data_file: '{mtdir}/allele_data.ht'
+    allele_counts_file: '{mtdir}/qc_ac.ht'
+    inbreeding_file: '{mtdir}/inbreeding.ht'
+    mtfile: '{mtdir}/mt_varqc_splitmulti.mt'
+    htoutfile_rf_all_cols: '{mtdir}/ht_for_RF_all_cols.ht'
+    htoutfile_rf_var_type_all_cols: '{mtdir}/ht_for_RF_by_variant_type_all_cols.ht'
+
+  # --- Step 3.3 --- #
+  rf_test_interval: chr20 # used in multiple functions
+  runs_json: '{rfdir}/rf_runs.json'
+
+  train_rf:
+    input_ht_file: '{mtdir}/ht_for_RF_by_variant_type_all_cols.ht'
+    gnomad_train_rf_fp_to_tp: 1.0
+    gnomad_train_rf_num_trees: 500
+    gnomad_train_rf_max_depth: 5
+
+  # --- Step 3.4 --- #
+  # only var_qc_rf_dir (which is CVAR) is required
+
+  # --- Step 3.5 --- #
+  add_cq_annotation:
+    synonymous_file: '{resdir}/synonymous_variants.txt'
+
+  dnm_and_family_annotation:
+    dnm_htfile: '{mtdir}/denovo_table.ht'
+    fam_stats_htfile: '{mtdir}/family_stats.ht'
+    trio_stats_htfile: '{mtdir}/trio_stats.ht'
+
+  transmitted_singleton_annotation:
+    trio_mtfile: '{mtdir}/trios.mt'
+    trio_filtered_mtfile: '{mtdir}/trios_filtered_.mt'
+
+  annotate_gnomad:
+    gnomad_htfile: '{resdir}/gnomad.exomes.r2.1.1.sites.liftover_grch38.ht'
+
+  
+  # --- Step 3.6 --- #
+  add_rank:
+    subrank_expr_de_novo_high_quality_rank: 0.9
+    subrank_expr_de_novo_medium_quality_rank: 0.5
+
+  create_binned_data_initial:
+    truth_htfile: '{resdir}/truthset_table.ht'
+
+    high_quality_p_de_novo: 0.99
+    medium_quality_p_de_novo: 0.5
+
+    # TODO: merge these into a single parameter?
+    n_trans_common_gnomad_af: 0.1
+    n_untrans_common_gnomad_af: 0.1
+
+  
+  # --- Step 3.7 --- #
+  create_plots:
+    qc_plots_settings:
+      mean_point_size: 4.0
+      min_point_size: 1.0
+      max_point_size: 16.0
+      label_text_font_size: "14pt"
+      title_text_font_size: "16pt"
+      subtitle_text_font_size: "14pt"
+      axis_axis_label_text_font_size: "16pt"
+      axis_axis_label_text_font_style: "normal"
+      axis_major_label_text_font_size: "14pt"
+
+
+  # --- Step 3.8 --- #
+  # no config parameters used
+
+  # --- Step 3.9 --- #
+  annotate_mt_with_cq_rf_score_and_bin:
+    mtfile: '{mtdir}/mt_varqc_splitmulti.mt'
+    cqfile: '{resdir}/all_consequences.txt'
+    mtoutfile_after_varqc: '{mtdir}/mt_after_var_qc.mt'
+
+evaluation:
+  giab_vcf: '{resdir}/HG001_GRCh38_benchmark.interval.illumina.vcf.gz'
+  giab_cqfile: '{resdir}/all.interval.illumina.vep.info.txt'
+  giab_sample: null
+  snp_bins: []
+  indel_bins: []
+  gq_vals: [10, 15, 20]
+  dp_vals: [5, 10]
+  ab_vals: [0.2, 0.3]
+  missing_vals: [0, 0.5, 0.9, 0.95]
+  snp_json: '{anndir}/evaluation.snp.json'
+  snp_tsv_filesuffix: '_genotype_hard_filter_comparison_snv.txt'
+  indel_json: '{anndir}/evaluation.indel.json'
+  indel_tsv_filesuffix: '_genotype_hard_filter_comparison_indel.txt'
+
+step4:
+  # --- Step 4.1 --- #
+  filter_mt:
+    mtfile: '{mtdir}/mt_after_var_qc.mt'
+    mtoutfile_filtered: '{mtdir}/mt_after_var_qc_hard_filter_gt.mt'
+
+  # --- Step 4.1a --- #
+
+  annotate_cq_rf:
+    mtfile: '{mtdir}/mt_varqc_splitmulti.mt'
+    cqfile: '{resdir}/all_consequences_with_gene_and_csq.txt'
+
+  apply_hard_filters:
+    hard_filters:
+      missingness: 0.5
+      snp:
+        relaxed:
+          bin: 92
+          dp: 5
+          gq: 10
+          ab: 0.2
+        medium:
+          bin: 88
+          dp: 5
+          gq: 10
+          ab: 0.2
+        stringent:
+          bin: 84
+          dp: 5
+          gq: 15
+          ab: 0.2
+      indel:
+        relaxed:
+          bin: 68
+          dp: 5
+          gq: 10
+          ab: 0.2
+        medium:
+          bin: 66
+          dp: 5
+          gq: 15
+          ab: 0.2
+        stringent:
+          bin: 58
+          dp: 5
+          gq: 20
+          ab: 0.3
+
+  # used as an output of the whole step
+  mtoutfile_annot: '{mtdir}/mt_hard_filter_combinations.mt'
+
+  # --- Step 4.2 --- #
+  annotate_gnomad:
+    # mtfile: '{mtdir}/mt_after_var_qc_hard_filter_gt.mt' # used when 1-apply_hard_filters is run
+    mtfile: '{mtdir}/mt_hard_filter_combinations.mt' # used when 1a-apply_hard_filters is run
+    gnomad_htfile: '{resdir}/gnomad.exomes.r2.1.1.sites.liftover_grch38.ht'
+
+  get_trans_untrans_synon_singleton_counts:
+    pedfile: '{resdir}/trios.ped'
+
+  get_counts_per_cq:
+    cqfile: '{pltdir}/variant_counts_per_cq_post_qc.txt'
+  
+  get_ca_fractions:
+    cafile: '{pltdir}/frac_ca_per_sample_post_qc_snv.txt'
+
+  # --- Step 4.3 --- #
+  export_vcfs:
+    mtfile_filtered: '{mtdir}/mt_after_var_qc_hard_filter_gt.mt'
+    # TODO: after adopting new config render change to substitution
+    vcf_output_dir: '/lustre/scratch126/dh24_test/wes-qc/tests/filtered_vcfs/' 
+
+  # --- Step 4.3a --- #
+  export_vcfs_a:
+    mtfile: '{mtdir}/mt_hard_filter_combinations.mt'
+    vcf_output_dir: '/lustre/scratch126/dh24_test/wes-qc/tests/filtered_vcfs_combinations/'
+
+  # --- Ster 4.3b --- #
+  export_vcfs_b:
+    mtfile: '{mtdir}/mt_hard_filter_combinations.mt'
+    filtered_vcf_dir: '/lustre/scratch126/dh24_test/wes-qc/tests/filtered_vcfs_combinations_stringent/'
diff --git a/docs/hail-on-spark.md b/docs/hail-on-spark.md
new file mode 100644
index 0000000..29197ed
--- /dev/null
+++ b/docs/hail-on-spark.md
@@ -0,0 +1,268 @@
+# Getting Started With Hail On Openstack
+
+> [!WARNING]
+> This documentation is under development and may be incomplete.
+
+This tutorial describes how to initiate a cluster on **Openstack** suitable for running **Hail**. 
+
+The command line tool [osdataproc](https://github.com/wtsi-hgi/osdataproc/) is used to create an openstack cluster with [Apache Spark](https://spark.apache.org/)  and [Apache Hadoop](https://hadoop.apache.org/) configured. The cluster is provisioned with [Jupyterlab](https://jupyter.org/) for interactive computing, [Hail](https://hail.is/) for genomic analysis, and [Netdata](https://www.netdata.cloud/) for monitoring. 
+## Install `osdataproc`
+This part of work is done on your local machine.
+
+> [!NOTE]
+The `osdataproc` utility requires python 3.9. Before proceeding, ensure that you're using the correct Python version. Ensure that the Python version is correct:
+>```shell
+>python --version
+>```
+>
+>The easiest way to install the correct Python version is using [Conda](https://docs.conda.io/en/latest/).
+>```shell
+>conda create -n py39 python=3.9
+>conda activate py39
+> ``` 
+>or  install the correct Python version locally:
+>``` shell
+>wget https://www.python.org/ftp/python/3.9.8/Python-3.9.8.tgz
+>tar -zxvf Python-3.9.8.tgz
+>cd Python-3.9.8/
+>mkdir ~/.localpython
+># Prepare the environment for building
+>./configure --prefix=$HOME/.localpython
+># Building the system
+> make
+> # Implement the installation
+>make install
+>```
+>Running the code above will install python 3.9.8 at `~/localpython/bin/python3.9`
+
+### Create and activate the Python virtual environment for `osdataproc`
+
+Set up a virtual environment with newly installed Python.
+```bash
+virtualenv osdataproc_env -p path/to/python3.9
+# activate
+source osdataproc_env/bin/activate
+# deactivate with simply `deactivate`
+```
+
+### Install Terraform
+
+`osdataproc` requires [Terraform](https://www.terraform.io/) version 1.4 or higher. Find the location of the latest Terraform [here](https://developer.hashicorp.com/terraform/downloads?product_intent=terraform), download and unzip into a location on your path. The easy way is to use the `bin` folder of the environment created above. You should download archive for amd64, it works on M1/M3 MacBooks.
+
+```bash
+cd osdataproc_env/bin
+wget https://releases.hashicorp.com/terraform/1.9.3/terraform_1.9.3_linux_386.zip
+unzip terraform_1.8.2_darwin_amd64.zip
+cd ../..
+```
+
+### Install osdataproc
+
+Clone the `osdataproc` git repository in a separate folder on your machine, and install it via `pip`.
+
+```bash 
+git clone https://github.com/wtsi-hgi/osdataproc.git
+cd osdataproc
+pip install -e .
+cd ..
+```
+
+Check, that `osdataproc` installed successfully:
+```shell
+osdataproc create --help
+```
+
+> [!WARNING]
+Terraform stores all cluster configuration data in the  `./terraform/terraform.tfstate.d` folder in the `osdataproc` folder. **Don't remove it**. Otherwise, you lose access to cluster configuration and won't be able to suspen/resume/destroy created clusters.
+
+>[!TIP]
+>If when installing `osdataproc` the wheel fail to be built, try updating `wheel` and `setuptools` packages.
+>``` shell
+>pip install wheel -U # 0.43.0 version
+>pip install setuptools -U # 71.1.0 version
+>```
+
+## Managing a cluster
+### Create a cluster
+
+For naming your clusters and volumes, we recommend prefixing with your username, similarly for your volumes (nfs-volume).
+**Example:** `gz3-hail`
+
+You will be prompted for a password, this password is used for accessing Jupyter and Spark master node. Since you may have to swap clusters or allow other people to access this password needs to be something you are happy to share with others.
+
+**Example**: To create a cluster using 50 `m2.medium` workers 
+and create a new volume called `gz3-hail` run the following script:
+
+```shell
+eval `ssh-agent -s` \
+ssh-add path/to/public/key
+
+osdataproc create [--num-workers]    <Number of desired worker nodes>
+                  [--public-key]     <Path to public key file>
+                  [--flavour]        <OpenStack flavour to use>
+                  [--network-name]   <OpenStack network to use>
+                  [--lustre-network] <OpenStack Lustre provider network to use>
+                  [--image-name]     <OpenStack image to use - Ubuntu images only>
+                  [--nfs-volume]     <Name/ID of volume to attach or create as NFS shared volume>
+                  [--volume-size]    <Size of OpenStack volume to create>
+                  [--device-name]    <Device mountpoint name of volume>
+                  [--floating-ip]    <OpenStack floating IP to associate to master node - will automatically create one if not specified>
+                  <cluster_name>
+```
+
+Wait until Terraform completes cluster creation. The creation of clusters can take some time and needs your laptop to be connected to the network.
+
+>[!IMPORTANT]
+>The IP address of your new cluster will be printed to STDOUT. **Save it somewhere**.
+
+When the cluster completion finishes, inspect the log. There should be no failed tasks:
+### Destructing and re-creating cluster
+There are many reasons, why the cluster creation can fail. 
+In most cases, it's easier to delete and re-create the cluster.
+
+To delete cluster, run the following command:
+```bash
+osdataproc destroy "${cluster_name}"
+```
+
+To re-create cluster, run the same command without specifying `--volume-size`. The new cluster will use existing volume. In most cases, volumes are created correctly, so you don't need to delete and re-create it.
+## Running Hail tasks on the cluster
+
+Log into your new cluster using the IP address created when your new cluster was created. For example:
+
+```bash
+ssh ubuntu@<public_ip>
+```
+
+### Installing additional software
+
+The WES-QC code requires Python GnomaAD package. To install it, run the following:
+
+```shell
+sudo apt install postgresql python3.9-dev libpq-dev
+pip install gnomad
+```
+
+### Check cluster status
+To check the cluster status use the SPARK web interface:
+<http://<public_ip>/spark/>
+
+### Submit Hail scripts
+
+Hail scripts are submitted to worker nodes using spark as follows:
+
+```bash
+export PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python 
+spark-submit /path/to/hail_script.py
+```
+
+Alternatively, you can activate environment and use spark commands directly
+
+```bash
+source /home/ubuntu/venv/bin/activate
+spark-submit /path/to/hail_script.py
+```
+
+It is highly advisable to open `tmux` or `screen` session before submitting spark jobs.
+
+### Access Jupyter
+
+Jupyter can be accessed via a web browser as follows (using the IP address created when you created your new cluster):
+<https://<public_ip>/jupyter/lab>
+
+You will be prompted for a password that you used to create the cluster.
+
+>[!WARNING]
+All Hail tasks (both command-line and interactive via Jupyter) occupy all working nodes. You can't run Jupyter notebook and command-lite script simultaneously. 
+>
+>To kill a Jupyter job, shut down all Jupyter kernels, or kill the `Hail` process via Spark master web interface.
+
+<!--### Workaround netdata log issue
+Often the netdata access logs grow too fast. To avoid running out of free space, we suggest changing logrotate settings.
+
+First, change the logrotate schedule:
+```shell
+sudo ln -s /etc/cron.daily/logrotate /etc/cron.hourly/logrotate
+```
+
+Then, add the following lines to the `/etc/logrotate.d/netdata` file:
+```
+/var/log/netdata/*.log {
+        maxsize 1G
+        hourly
+        rotate 1
+        ...
+}
+```
+
+Finally, run Logrotate manually to ensure that it works without errors
+```shell
+sudo logrotate /etc/logrotate.d/netdata
+```
+
+## Troubleshooting
+
+### Cleaning up Netdata logs
+
+In case if you cluster reports `No space left on the device`
+the most probable source of this issue is netdata logs. 
+To inspect it, go to the netdata folder, and check the log files size:
+```shell
+cd /var/log/netdata
+ls -lh
+```
+
+If the size of netdata logs is too big, remove it:
+```shell
+sudo rm -rf *.log.*
+```
+
+### Resetting HDFS safe mode
+
+In case of an issue with the free space on the device (both caused by local FS overflow or by Lustre quota)
+the HDFS will switch in the safe mode. The Hail processing will throw the error message:
+`Caused by: org.apache.hadoop.ipc.RemoteException(org.apache.hadoop.hdfs.server.namenode.SafeModeException): 
+Cannot create directory /shared/spark-logs. Name node is in safe mode.
+`
+
+To continue working with Hail, you need to manually move it bach to operational mode. To do it:
+1. Deal with the absence of free space (clean up logs, temporary folders, unused matrixtables, etc.). 
+2. Turn HDFS bach to the operational mode:
+
+```shell
+hdfs dfsadmin -safemode leave
+```
+
+### Manual cluster cleanup
+In the case of cluster creation/destruction failure (for example, due to connection loss),
+`osdataproc` may not be able to clean up all cluster resources. 
+
+To manually clean up all requested resources via Theta, do the following, do the following:
+
+>[!WARNING]
+Working under the project user, you can delete resources belonging to other project members.
+>
+>Please, be cautious and double-check every step.
+
+1. Log in to [Theta](https://theta.internal.sanger.ac.uk/project/)
+2. Choose the project under `Projects`
+3. Clean up instances
+   1. Navigate to `instances`
+   2. Set the filter by the instance name and find all instances from your cluster
+   3. **Double check, that you selected only instances belonging to your cluster**
+   4. Remove instances
+4. Clean up Lustre network ports
+   1. Navigate to `Networks`
+   2. Choose the secure Lustre network
+   3. Go to the `Ports` tab
+   4. Set the filter and find all ports from your cluster
+   5. **Double check, that you selected only ports belonging to your cluster**
+   6. Remove ports
+5. Clean up Cloudforms network
+   1. Navigate to `Networks`
+   2. Choose the Cloudforms network
+   3. Remove ports the same way as yu did in point 4
+6. Remove cluster security groups:
+   1. Navigate to `Security groups`
+   2. Set the filter two security groups created for the cluster.
+   3. Remove security groups -->
\ No newline at end of file
diff --git a/docs/wes-qc-concepts.md b/docs/wes-qc-concepts.md
new file mode 100644
index 0000000..e1c1022
--- /dev/null
+++ b/docs/wes-qc-concepts.md
@@ -0,0 +1,49 @@
+---
+tags:
+  - Concept
+  - Compute
+  - Farm
+  - Pipelines
+---
+
+# WES QC
+
+The aim of WES QC is to produce a clean dataset removing problem samples, and excluding variants and genotypes that are liekely to be false positives. Each dataset is different and the QC requires careful tailoring and evaluation at each step to ensure that it is appropriate for the dataset being worked on.
+
+## Overview
+
+WES QC consists of three main steps: Sample QC, variant QC and genotype QC. It is written using (Hail)[https://hail.is/] and much of it is based on methods used by gnomAD:
+
+https://gnomad.broadinstitute.org/news/2018-10-gnomad-v2-1/  
+https://gnomad.broadinstitute.org/news/2019-10-gnomad-v3-0/  
+https://gnomad.broadinstitute.org/news/2020-10-gnomad-v3-1-new-content-methods-annotations-and-data-availability/
+
+
+## Sample QC
+
+The aim of sample QC is to remove poor quality samples. These may be samples where the sequencing is poor quality, these may be contaminated samples or these may be samples for which the identity is in question.
+
+### Stratified sample QC
+
+The superpopulation each sample belongs to is inferred using PCA. Outliers are identified within each population for each metric tested: 
+- Number of SNPs  
+- Number of deletions  
+- Number of insertions  
+- Insertion/deletion ratio  
+- Heterozygosity rate  
+- Heterozygous/homozygous ratio  
+- Number of transitions  
+- Number of transversions  
+- Transition/transversion ratio.
+
+### Contaminated samples
+
+freemix
+
+### Sample identity
+
+gtcheck
+
+## Variant QC
+
+## Genotype QC
diff --git a/docs/wes-qc-hail.md b/docs/wes-qc-hail.md
new file mode 100644
index 0000000..71a012f
--- /dev/null
+++ b/docs/wes-qc-hail.md
@@ -0,0 +1,226 @@
+# Getting Started With WES QC Using Hail
+
+> [!WARNING]
+> This documentation is under development and may be incomplete.
+
+This guide covers WES QC using Hail. It is important to note that every dataset is different and that for best results it is not advisable to view this guide as a recipe for QC. Each dataset will require careful tailoring and evaluation of the QC for best results.
+
+## Before you start
+
+In order to run through this guide you will need an OpenStack cluster with Hail and Spark installed. It is recommended that you use `osdataproc` to create this. Follow the [[hail-on-spark]] guide to create such a cluster.
+
+This guide also requires a WES dataset joint called with GATK using the cromwell pipeline. If starting with a Hail matrixtable then start at Step [[#2. Sample QC]].
+
+## Set up
+
+Each dataset should have its own branch of the WES QC code. Clone the main branch using:
+```shell
+git clone https://github.com/wtsi-hgi/wes-qc.git
+```
+
+Create a new branch and switch to your branch:
+
+``` shell
+cd wes_qc
+git checkout -b my_project
+```
+
+Edit `config/inputs.yaml` to include the correct paths for your datasets and working directories. ==You will need to edit all directory paths in this file and commit/push your changes to git.==
+
+Start a new tmux session, and edit the PYTHONPATH to include the directory you originally cloned the git repo into.
+
+``` shell
+export PYTHONPATH=/path/to/wes-qc
+```
+
+>[!NOTE]
+>To submit jobs to spark one can either:
+>```shell
+># OPTION 1
+>export PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python 
+># OPTION 2
+>source /home/ubuntu/venv/bin/activate
+>
+>spark-submit /path/to/hail_script.py
+>```
+
+### 1. Load data from VCFs into Hail
+
+Load VCFs into Hail and save as a Hail MatrixTable
+
+```shell
+spark-submit 1-import_data/1-import_gatk_vcfs_to_hail.py
+```
+
+### 2. Sample QC
+
+1. Apply hard filters and annotate with imputed sex
+
+``` shell
+spark-submit 2-sample_qc/1-hard_filters_sex_annotation.py
+```
+
+2. Prune by linkage disequilibrium, and identify samples from related individuals with PCrelate
+
+```shell
+spark-submit 2-sample_qc/2-prune_related_samples.py
+```
+
+The following four steps deal with prediction of superpopulation by PCA and projection on to 1000 genomes data of known population. If a matrixtable of 1000 genomes data is available the first step can be omitted.
+
+3. Population prediction with PCA
+
+Create MatrixTable from 1kg WES VCFs.
+
+``` shell
+spark-submit 2-sample_qc/3-population_pca_prediction.py --kg_to_mt
+```
+
+Merge 1kg MatrixTable with WES MatrixTable.
+
+``` shell
+spark-submit 2-sample_qc/3-population_pca_prediction.py --merge
+```
+
+Annotate with known populations for 1kg samples and filter to remove low quality variants, variants in long range linkage disequilibrium regions and palindromic SNPs
+
+``` shell
+spark-submit 2-sample_qc/3-population_pca_prediction.py --filter
+```
+
+Run PCA.
+
+``` shell
+spark-submit 2-sample_qc/3-population_pca_prediction.py --pca
+```
+
+Run population prediction.
+
+``` shell
+spark-submit 2-sample_qc/3-population_pca_prediction.py --assign_pops
+```
+
+Use a Jupyter Notebook on the Hail cluster to plot PC1 vs PC2 and PC1 vs PC3 for known populations (1000 genomes only) and predicted populations. An example Jupyter Notebook is in *jupyter_notebooks/sample_qc/population_inference_plots.ipynb*
+
+4. Outliers identification
+
+Now that we have the predicted populations that each sample belongs to we can run sample QC stratified by population and identify outliers within each population for each metric tested:
+- number of SNPs
+- number of deletions and insertions, insertion/deletion ratе
+- heterozygosity rate, heterozygous/homozygous ratio
+- number of transitions and transversions, transition/transversion ratio.
+
+``` shell
+spark-submit 2-sample_qc/4-find_population_outliers.py
+```
+
+5. Filter data to exclude samples which fail QC. 
+
+The final step in sample QC is filtering the data to remove samples which are identified as failing in the previous script. <!At this stage samples failing on FREEMIX score and on identity checks are also removed. This samples should be in files in the annotations directory: `verify_bam_id_result_concat.selfSM` lists sample ID and FREEMIX score and `sanger_samples_excluded_after_gtcheck.txt` lists samples failing identity checks. If no samples fail identify checks the latter file could be empty.> These samples are saved in `samples_failing_qc.tsv.bgz` in the annotation directory.
+
+``` shell
+spark-submit 2-sample_qc/5-filter_fail_sample_qc.py
+```
+
+### 3. Variant QC
+
+Variant QC requires a ped file detailing any trios. This is an unheaded, tab-delimited file that contains the following columns:
+- Family ID
+- Proband ID
+- Paternal ID
+- Maternal ID
+- Proband sex (1 or 2)
+- Proband affected status (0 or 1)
+
+The first step of variant QC produces a truth set of known true positive variants and generates annotation.
+
+``` shell
+spark-submit 3-variant_qc/1-generate_truth_sets.py --all
+```
+
+Next an input table is generated to run the random forest on.
+
+``` shell
+spark-submit 3-variant_qc/2-create_rf_ht.py
+```
+
+Next train the random forest model, note the use of --master local[*] here which is needed to ensure that the worker nodes pick up the correct python modules.
+
+``` shell
+spark-submit --master local[*] 3-variant_qc/3-train_rf.py
+```
+
+A run hash ID will be printed to STDOUT, this is needed for future steps, so note it down. It is an 8 character string consisting of letters and numbers and is represented in the following commands as run_hash.
+
+Now apply the random forest to the entire dataset.
+
+``` shell
+spark-submit --master local[*] 3-variant_qc/4-apply_rf.py --runhash run_hash
+```
+
+Annotate the random forest output with metrics including synonymous variants, family annotation, transmitted/untransmitted singletons and gnomAD allele frequency. Synonymous variants are required in a file generated from VEP annotation and in the following format:
+
+```
+chr10   100202145   rs200461553 T   G   synonymous_variant  
+chr10   100204510   rs2862988   C   T   synonymous_variant  
+chr10   100204528   rs374991603 G   A   synonymous_variant  
+chr10   100204555   rs17880383  G   A   synonymous_variant  
+```
+
+``` shell
+spark-submit 3-variant_qc/5-annotate_ht_after_rf.py  --runhash run_hash
+```
+
+Add ranks to variants based on random forest score, and bin the variants based on this.
+
+``` shell
+spark-submit 3-variant_qc/6-rank_and_bin.py --runhash run_hash
+```
+
+Create plots of the binned random forest output to use in the selection of thresholds. Separate thresholds are used for SNPs and indels.
+
+``` shell
+spark-submit 3-variant_qc/7-plot_rf_output.py --runhash run_hash
+```
+
+After examining the plots and selecting suitable thresholds for SNPs and indels you can calculate the number of true positive and false positive variants remaining at your chosen thresholds and at the bins surrounding it using the following (where snp_bin and indel_bin are the thresholds selected for SNPs and indels respectively).
+
+``` shell
+spark-submit 3-variant_qc/8-select_thresholds.py --runhash run_hash --snv snp_bin --indel indel_bin
+```
+
+Filter the variants in the Hail MatrixTable based on the selected threshold for SNPs and indels
+
+``` shell
+spark-submit 3-variant_qc/9-filter_mt_after_variant_qc.py --runhash run_hash --snv snp_bin --indel indel_bin
+```
+
+### 4. Genotype QC
+
+Genotype QC may be performed using a range of filters defined in *config/inputs.yaml* or it may be performed using a single set of filters for DP, GQ, VAF and bins. Here we apply a range of filters (relaxed, medium and stringent) which we have defined in the *config/inputs.yaml* file
+
+``` shell
+spark-submit 4-genotype_qc/1a-apply_range_of_hard_filters.py --runhash run_hash
+```
+
+In order to evaluate these filters, variant counts per consequence per sample and transmitted/untransmitted ratio of synonymous singletons (if trios are present in the data) are calculated as follows. VEP annotation is required for this step in the following format:
+
+```
+chr10   100199947   rs367984062 A   C   intron_variant  
+chr10   100199976   rs774723210 G   A   missense_variant  
+chr10   100200004   .   C   A   missense_variant  
+chr10   100200012   rs144642900 C   T   missense_variant  
+chr1    100200019   .  C    A   stop_gained&splice_region_variant  
+```
+
+``` shell
+spark-submit 4-genotype_qc/2-counts_per_sample.py
+```
+
+Export the filtered variants to VCF.
+
+``` shell
+spark-submit 4-genotype_qc/3-export_vcfs.py
+```
+
+
diff --git a/evaluation/compare_hard_filter_combinations.py b/evaluation/compare_hard_filter_combinations.py
index 87646d1..761e85c 100755
--- a/evaluation/compare_hard_filter_combinations.py
+++ b/evaluation/compare_hard_filter_combinations.py
@@ -2,10 +2,11 @@
 import os.path
 import hail as hl
 import pyspark
-import datetime
 import argparse
 import json
-from utils.utils import parse_config
+import logging
+from typing import Optional
+from utils.utils import parse_config, path_spark
 from utils.utils import select_founders, collect_pedigree_samples
 
 
@@ -76,6 +77,7 @@ def prepare_giab_ht(giab_vcf: str, giab_cqfile: str, mtdir: str) -> hl.Table:
     :param str mtdir: MatrixTable directory
     :return: hl.Table
     '''
+    logging.info("Preparing GiaB HailTable")
     mt = hl.import_vcf(giab_vcf, force_bgz=True, reference_genome='GRCh38')
     mt = hl.variant_qc(mt)
     mt = mt.filter_rows(mt.variant_qc.n_non_ref > 0)
@@ -92,8 +94,8 @@ def prepare_giab_ht(giab_vcf: str, giab_cqfile: str, mtdir: str) -> hl.Table:
 
     mt = mt.annotate_rows(consequence=ht[mt.row_key].consequence)
     giab_vars = mt.rows()
-    tmphtg = mtdir + "tmphtgx.ht"
-    giab_vars = giab_vars.checkpoint(tmphtg, overwrite = True)
+    tmphtg = path_spark(os.path.join(mtdir, "tmphtgx.ht"))
+    giab_vars = giab_vars.checkpoint(tmphtg, overwrite=True)
 
     return giab_vars
 
@@ -119,19 +121,18 @@ def annotate_cq(mt: hl.MatrixTable, cqfile: str) -> hl.MatrixTable:
     return mt
 
 
-def filter_and_count(mt_path: str, ht_giab: hl.Table, pedfile: str, mtdir: str) -> dict:
+def filter_and_count(mt_path: str, ht_giab: hl.Table, pedfile: str, mtdir: str, config: dict) -> dict:
     '''
-    Filter MT by various bins followed by genotype GQ and cauclate % of FP and TP remaining for each bifn
-    :param hl.MatrixTable mt_tp: Input TP MatrixTable
-    :param hl.MatrixTable mt_fp: Input FP MatrixTable
-    :param hl.MatrixTable mt_syn: Input synonymous MatrixTable
-    :param hl.MatrixTable mt_prec_recall: mt from GIAB sample for precision/recall analysys
+    Filter MT by various bins followed by genotype GQ and calculate % of FP and TP remaining for each bin
     :param hl.Table ht_giab: GIAB variants
-    :param str plot_dir: directory for output files 
     :param str mtdir: matrixtable directory
+    :param mt_path: path to matrixtable
+    :param pedfile: path to trio file
+    :param config: config object
     :return: dict
     '''
     results = {'snv': {}, 'indel': {}}
+    giab_sample = config['evaluation']['giab_sample']
 
     mt = hl.read_matrix_table(mt_path)
     pedigree = hl.Pedigree.read(pedfile)
@@ -142,78 +143,79 @@ def filter_and_count(mt_path: str, ht_giab: hl.Table, pedfile: str, mtdir: str)
     mt_snp_path = os.path.join(mtdir, 'tmp.hard_filters_combs.snp.mt')
     mt_snp = mt_snp.checkpoint(mt_snp_path, overwrite=True)
 
-    snp_mt_tp, snp_mt_fp, _, _ = filter_mts(mt_snp, mtdir=mtdir)
+    snp_mt_tp, snp_mt_fp, _, _ = filter_mts(mt_snp, mtdir=mtdir, giab_sample=None)
     results['snv_total_tp'] = snp_mt_tp.count_rows()
     results['snv_total_fp'] = snp_mt_fp.count_rows()
 
-    snp_bins = [80, 82, 84, 86, 88, 90]
-    indel_bins = [58, 60, 62, 64, 66, 68]
-    gq_vals = [10, 15, 20]
-    dp_vals = [5, 10]
-    ab_vals = [0.2, 0.3]
-    missing_vals = [0, 0.5, 0.9, 0.95]
+    snp_bins = config['evaluation']['snp_bins']
+    indel_bins = config['evaluation']['indel_bins']
+    gq_vals = config['evaluation']['gq_vals']
+    dp_vals = config['evaluation']['dp_vals']
+    ab_vals = config['evaluation']['ab_vals']
+    missing_vals = config['evaluation']['missing_vals']
 
     for bin in snp_bins:
-        bin_str = "bin_" + str(bin)
-        print("bin " + str(bin))
+        bin_str = f"bin_{bin}"
+        logging.info(f"bin {bin}")
         mt_snp_bin = mt_snp.filter_rows(mt_snp.info.rf_bin <= bin)
 
         for dp in dp_vals:
-            dp_str = 'DP_' + str(dp)
+            dp_str = f'DP_{dp}'
             for gq in gq_vals:
-                gq_str = 'GQ_' + str(gq)
+                gq_str = f'GQ_{gq}'
                 for ab in ab_vals:
-                    ab_str = 'AB_' + str(ab)
+                    ab_str = f'AB_{ab}'
                     for call_rate in missing_vals:
                         missing_str = f'missing_{call_rate}'
-                        print(dp_str + " " + gq_str + " " + ab_str + " " + missing_str)
-                        filter_name = ("_").join([bin_str, dp_str, gq_str, ab_str, missing_str])
+                        logging.info(f'{dp_str} {gq_str} {ab_str} {missing_str}')
+                        filter_name = "_".join([bin_str, dp_str, gq_str, ab_str, missing_str])
 
                         mt_snp_hard = apply_hard_filters(mt_snp_bin, dp=dp, gq=gq, ab=ab, call_rate=call_rate)
                         mt_snp_hard_path = os.path.join(mtdir, 'tmp.hard_filters_combs.snp-hard.mt')
                         mt_snp_hard = mt_snp_hard.checkpoint(mt_snp_hard_path, overwrite=True)
 
-                        mt_tp_tmp, mt_fp_tmp, mt_syn_tmp, mt_prec_recall_tmp = filter_mts(mt_snp_hard, mtdir=mtdir)
+                        mt_tp, mt_fp, mt_syn, mt_prec_recall = filter_mts(mt_snp_hard, mtdir=mtdir, giab_sample=giab_sample)
 
-                        snp_counts = count_tp_fp_t_u(mt_tp_tmp, mt_fp_tmp, mt_syn_tmp, mt_prec_recall_tmp, ht_giab, pedigree, 'snv', mtdir)
+                        snp_counts = count_tp_fp_t_u(mt_tp, mt_fp, mt_syn, mt_prec_recall, ht_giab, pedigree, 'snv', mtdir)
                         results['snv'][filter_name] = snp_counts
 
-                        with open('/lustre/scratch123/qc/BiB/evaluation.snp.json', 'w') as f:
+                        with open(config['evaluation']['snp_json'], 'w') as f:
                             json.dump(results, f)
 
     mt_indel_path = os.path.join(mtdir, 'tmp.hard_filters_combs.indel.mt')
-    mt_indel = mt_indel.repartition(mt.n_partitions() // 4).checkpoint(mt_indel_path, overwrite=True)
+    n_partitions = max(1, mt.n_partitions() // 4)
+    mt_indel = mt_indel.repartition(n_partitions).checkpoint(mt_indel_path, overwrite=True)
 
-    indel_mt_tp, indel_mt_fp, _, _ = filter_mts(mt_indel, mtdir=mtdir)
+    indel_mt_tp, indel_mt_fp, _, _ = filter_mts(mt_indel, mtdir=mtdir, giab_sample=None)
     results['indel_total_tp'] = indel_mt_tp.count_rows()
     results['indel_total_fp'] = indel_mt_fp.count_rows()
 
     for bin in indel_bins:
-        bin_str = "bin_" + str(bin)
-        print("bin " + str(bin))
+        bin_str = f"bin_{bin}"
+        print(f"bin {bin}")
         mt_indel_bin = mt_indel.filter_rows(mt_indel.info.rf_bin <= bin)
 
         for dp in dp_vals:
-            dp_str = 'DP_' + str(dp)
+            dp_str = f'DP_{dp}'
             for gq in gq_vals:
-                gq_str = 'GQ_' + str(gq)
+                gq_str = f'GQ_{gq}'
                 for ab in ab_vals:
-                    ab_str = 'AB_' + str(ab)
+                    ab_str = f'AB_{ab}'
                     for call_rate in missing_vals:
                         missing_str = f'missing_{call_rate}'
                         print(dp_str + " " + gq_str + " " + ab_str + " " + missing_str)
-                        filter_name = ("_").join([bin_str, dp_str, gq_str, ab_str, missing_str])
+                        filter_name = "_".join([bin_str, dp_str, gq_str, ab_str, missing_str])
 
                         mt_indel_hard = apply_hard_filters(mt_indel_bin, dp=dp, gq=gq, ab=ab, call_rate=call_rate)
                         mt_indel_hard_path = os.path.join(mtdir, 'tmp.hard_filters_combs.indel-hard.mt')
                         mt_indel_hard = mt_indel_hard.checkpoint(mt_indel_hard_path, overwrite=True)
 
-                        mt_tp_tmp, mt_fp_tmp, mt_syn_tmp, mt_prec_recall_tmp = filter_mts(mt_indel_hard, mtdir=mtdir)
+                        mt_tp, mt_fp, mt_syn, mt_prec_recall = filter_mts(mt_indel_hard, mtdir=mtdir, giab_sample=giab_sample)
 
-                        indel_counts = count_tp_fp_t_u(mt_tp_tmp, mt_fp_tmp, mt_syn_tmp, mt_prec_recall_tmp, ht_giab, pedigree, 'indel', mtdir)
+                        indel_counts = count_tp_fp_t_u(mt_tp, mt_fp, mt_syn, mt_prec_recall, ht_giab, pedigree, 'indel', mtdir)
                         results['indel'][filter_name] = indel_counts
 
-                        with open('/lustre/scratch123/qc/BiB/evaluation.indel.json', 'w') as f:
+                        with open(config['evaluation']['indel_json'], 'w') as f:
                             json.dump(results, f)
 
     return results
@@ -240,7 +242,7 @@ def apply_hard_filters(mt: hl.MatrixTable, dp: int, gq: int, ab: float, call_rat
     return mt_tmp
 
 
-def count_tp_fp_t_u(mt_tp: hl.MatrixTable, mt_fp: hl.MatrixTable, mt_syn: hl.MatrixTable, mt_prec_recall: hl.Table, ht_giab: hl.Table, pedigree: hl.Pedigree, var_type: str, mtdir: str):
+def count_tp_fp_t_u(mt_tp: hl.MatrixTable, mt_fp: hl.MatrixTable, mt_syn: hl.MatrixTable, mt_prec_recall: Optional[hl.Table], ht_giab: hl.Table, pedigree: hl.Pedigree, var_type: str, mtdir: str):
     '''
     Filter mt by each rf bin in a list, then genotype hard filters and count remaining TP and P variants
     :param hl.MatrixTable mt_tp: Input TP MatrixTable
@@ -255,10 +257,7 @@ def count_tp_fp_t_u(mt_tp: hl.MatrixTable, mt_fp: hl.MatrixTable, mt_syn: hl.Mat
     '''
     results = {}
 
-    now = datetime.datetime.now()
-    print(now.time())
-
-    ht_prec_recall = mt_prec_recall.rows()
+    logging.debug(f'Executing count_tp_fp_t_u')
 
     counts = count_tp_fp(mt_tp, mt_fp)
     results['TP'] = counts[0]
@@ -266,18 +265,23 @@ def count_tp_fp_t_u(mt_tp: hl.MatrixTable, mt_fp: hl.MatrixTable, mt_syn: hl.Mat
 
     if var_type == 'snv':
         ratio = get_trans_untrans(mt_syn, pedigree, mtdir)
-        prec, recall = get_prec_recall(ht_prec_recall, ht_giab, 'snv', mtdir)
         results['t_u_ratio'] = ratio
-        results['prec'] = prec
-        results['recall'] = recall
-    else:
-        prec, recall, prec_frameshift, recall_frameshift, prec_inframe, recall_inframe = get_prec_recall(ht_prec_recall, ht_giab, 'indel', mtdir)
-        results['prec'] = prec
-        results['recall'] = recall
-        results['prec_inframe'] = prec_inframe
-        results['recall_inframe'] = recall_inframe
-        results['prec_frameshift'] = prec_frameshift
-        results['recall_frameshift'] = recall_frameshift
+
+    if mt_prec_recall is not None:
+        ht_prec_recall = mt_prec_recall.rows()
+
+        if var_type == 'snv':
+            prec, recall = get_prec_recall(ht_prec_recall, ht_giab, 'snv', mtdir)
+            results['prec'] = prec
+            results['recall'] = recall
+        else:
+            prec, recall, prec_frameshift, recall_frameshift, prec_inframe, recall_inframe = get_prec_recall(ht_prec_recall, ht_giab, 'indel', mtdir)
+            results['prec'] = prec
+            results['recall'] = recall
+            results['prec_inframe'] = prec_inframe
+            results['recall_inframe'] = recall_inframe
+            results['prec_frameshift'] = prec_frameshift
+            results['recall_frameshift'] = recall_frameshift
 
     return results
 
@@ -291,41 +295,39 @@ def get_prec_recall(ht_prec_recall: hl.Table, ht_giab: hl.Table, var_type: str,
     :param str mtdir: matrixtable directory
     :return: tuple
     '''
+    tmpht1 = os.path.join(mtdir, "tmppr1x.ht")
+    tmpht2 = os.path.join(mtdir, "tmppr2x.ht")
+    tmpht3 = os.path.join(mtdir, "tmppr3x.ht")
+    tmpht4 = os.path.join(mtdir, "tmppr4x.ht")
+    tmpht5 = os.path.join(mtdir, "tmppr5x.ht")
+    tmpht6 = os.path.join(mtdir, "tmppr6x.ht")
 
     if var_type == 'snv':
         giab_snvs = ht_giab.filter(hl.is_snp(ht_giab.alleles[0], ht_giab.alleles[1]))
         alspac_snvs = ht_prec_recall.filter(hl.is_snp(ht_prec_recall.alleles[0], ht_prec_recall.alleles[1]))
-        tmpht1 = mtdir + "tmppr1x.ht"
-        giab_snvs = giab_snvs.checkpoint(tmpht1, overwrite = True)
-        tmpht2 = mtdir + "tmppr2x.ht"
-        alspac_snvs = alspac_snvs.checkpoint(tmpht2, overwrite = True)
+        giab_snvs = giab_snvs.checkpoint(tmpht1, overwrite=True)
+        alspac_snvs = alspac_snvs.checkpoint(tmpht2, overwrite=True)
         p, r = calculate_precision_recall(giab_snvs, alspac_snvs)
         return p, r
 
     elif var_type == 'indel':
         giab_indels = ht_giab.filter(hl.is_indel(ht_giab.alleles[0], ht_giab.alleles[1]))
         alspac_indels = ht_prec_recall.filter(hl.is_indel(ht_prec_recall.alleles[0], ht_prec_recall.alleles[1]))
-        tmpht1 = os.path.join(mtdir, "tmppr1x.ht")
-        giab_indels = giab_indels.checkpoint(tmpht1, overwrite = True)
-        tmpht2 = os.path.join(mtdir, "tmppr2x.ht")
-        alspac_indels = alspac_indels.checkpoint(tmpht2, overwrite = True)
+        giab_indels = giab_indels.checkpoint(tmpht1, overwrite=True)
+        alspac_indels = alspac_indels.checkpoint(tmpht2, overwrite=True)
         p, r = calculate_precision_recall(giab_indels, alspac_indels)
 
         giab_frameshift = giab_indels.filter(giab_indels.consequence == 'frameshift_variant')
         alspac_frameshift = alspac_indels.filter(alspac_indels.consequence == 'frameshift_variant')
-        tmpht3 = os.path.join(mtdir, "tmppr3x.ht")
         giab_frameshift = giab_frameshift.checkpoint(tmpht3, overwrite = True)
-        tmpht4 = os.path.join(mtdir, "tmppr4x.ht")
         alspac_frameshift = alspac_frameshift.checkpoint(tmpht4, overwrite = True)
         p_f, r_f = calculate_precision_recall(giab_frameshift, alspac_frameshift)
 
         inframe_cqs = ['inframe_deletion', 'inframe_insertion']
         giab_in_frame = giab_indels.filter(hl.literal(inframe_cqs).contains(giab_indels.consequence))
         alspac_in_frame = alspac_indels.filter(hl.literal(inframe_cqs).contains(alspac_indels.consequence))
-        tmpht5 = os.path.join(mtdir, "tmppr5x.ht")
-        giab_in_frame = giab_in_frame.checkpoint(tmpht5, overwrite = True)
-        tmpht6 = os.path.join(mtdir, "tmppr6x.ht")
-        alspac_in_frame = alspac_in_frame.checkpoint(tmpht6, overwrite = True)
+        giab_in_frame = giab_in_frame.checkpoint(tmpht5, overwrite=True)
+        alspac_in_frame = alspac_in_frame.checkpoint(tmpht6, overwrite=True)
         p_if, r_if = calculate_precision_recall(giab_in_frame, alspac_in_frame)
 
         return p, r, p_f, r_f, p_if, r_if
@@ -375,12 +377,12 @@ def get_trans_untrans(mt: hl.MatrixTable, pedigree: hl.Pedigree, mtdir: str) ->
     mt_founders = hl.variant_qc(mt_founders, name='varqc_founders')
 
     mt2 = mt2.annotate_rows(varqc_trios=hl.Struct(AC=mt_founders.index_rows(mt2.row_key).varqc_founders.AC))
-    tmpmt3 = os.path.join(mtdir, "tmp3x.mt")
+    tmpmt3 = os.path.join(mtdir, "tmp1x.mt")
     mt2 = mt2.checkpoint(tmpmt3, overwrite=True)
 
     # split to potentially transmitted/untransmitted
     trans_mt = mt2.filter_rows(mt2.varqc_trios.AC[1] == 1)
-    tmpmt5 = os.path.join(mtdir, "tmp5x.mt")
+    tmpmt5 = os.path.join(mtdir, "tmp2x.mt")
     trans_mt = trans_mt.checkpoint(tmpmt5, overwrite=True)
 
     # run tdt function for potential trans and untrans
@@ -409,17 +411,17 @@ def count_tp_fp(mt_tp: hl.MatrixTable, mt_fp: hl.MatrixTable) -> tuple:
     return tp_count, fp_count
 
 
-def filter_mts(mt: hl.MatrixTable, mtdir: str) -> tuple:
+def filter_mts(mt: hl.MatrixTable, mtdir: str, giab_sample: Optional[str] = None) -> tuple:
     '''
     Split matrixtable and return tables with just TP, just FP, just synonymous
     :param hl.MatrixTable mt: Input mtfile
     :param st mtdir: matrixtable directory
+    :param giab_sample: sample name of GiaB sample in cohort data
     :return: tuple of 4 hl.MatrixTable objects
     '''
     mt_true = mt.filter_rows(mt.TP == True)  # TP variants
     mt_false = mt.filter_rows(mt.FP == True)  # FP variants
     mt_syn = mt.filter_rows(mt.consequence == 'synonymous_variant')  # synonymous for transmitted/unstransmitted
-    sample = 'EGAN00004265526'  # GIAB12878/HG001
 
     tmpmtt = os.path.join(mtdir, "tp.mt")
     tmpmtf = os.path.join(mtdir, "fp.mt")
@@ -427,14 +429,17 @@ def filter_mts(mt: hl.MatrixTable, mtdir: str) -> tuple:
     tmpmtpr = os.path.join(mtdir, "pr.mt")
 
     mt_true = mt_true.checkpoint(tmpmtt, overwrite=True)
-    mt_false = mt_false.repartition(mt.n_partitions() // 10).checkpoint(tmpmtf, overwrite=True)
+    n_partitions = max(1, mt.n_partitions() // 10)
+    mt_false = mt_false.repartition(n_partitions).checkpoint(tmpmtf, overwrite=True)
     mt_syn = mt_syn.checkpoint(tmpmts, overwrite=True)
 
-    mt_prec_recall = mt.filter_cols(mt.s == sample)  # GIAB sample for precision/recall
-    mt_prec_recall = mt_prec_recall.filter_rows(mt_prec_recall.locus.in_autosome())
-    mt_prec_recall = hl.variant_qc(mt_prec_recall)
-    mt_prec_recall = mt_prec_recall.filter_rows(mt_prec_recall.variant_qc.n_non_ref > 0)
-    mt_prec_recall = mt_prec_recall.repartition(mt.n_partitions() // 10).checkpoint(tmpmtpr, overwrite=True)
+    mt_prec_recall = None
+    if giab_sample is not None:
+        mt_prec_recall = mt.filter_cols(mt.s == giab_sample)  # GIAB sample for precision/recall
+        mt_prec_recall = mt_prec_recall.filter_rows(mt_prec_recall.locus.in_autosome())
+        mt_prec_recall = hl.variant_qc(mt_prec_recall)
+        mt_prec_recall = mt_prec_recall.filter_rows(mt_prec_recall.variant_qc.n_non_ref > 0)
+        mt_prec_recall = mt_prec_recall.repartition(n_partitions).checkpoint(tmpmtpr, overwrite=True)
 
     return mt_true, mt_false, mt_syn, mt_prec_recall
 
@@ -466,16 +471,16 @@ def print_results(results: dict, outfile: str, vartype: str):
             outline = [var_f, tp, fp]
             if vartype == 'snv':
                 tu = str(results[vartype][var_f]['t_u_ratio'])
-                p = str(results[vartype][var_f]['prec'])
-                r = str(results[vartype][var_f]['recall'])
+                p = str(results[vartype][var_f].get('prec', ''))
+                r = str(results[vartype][var_f].get('recall', ''))
                 outline = outline + [tu, p, r]
             elif vartype == 'indel':
-                p = str(results[vartype][var_f]['prec'])
-                r = str(results[vartype][var_f]['recall']) 
-                p_f = str(results[vartype][var_f]['prec_frameshift'])
-                r_f = str(results[vartype][var_f]['recall_frameshift']) 
-                p_if = str(results[vartype][var_f]['prec_inframe'])
-                r_if = str(results[vartype][var_f]['recall_inframe']) 
+                p = str(results[vartype][var_f].get('prec', ''))
+                r = str(results[vartype][var_f].get('recall', ''))
+                p_f = str(results[vartype][var_f].get('prec_frameshift', ''))
+                r_f = str(results[vartype][var_f].get('recall_frameshift', ''))
+                p_if = str(results[vartype][var_f].get('prec_inframe', ''))
+                r_if = str(results[vartype][var_f].get('recall_inframe', ''))
                 outline = outline + [p, r, p_f, r_f, p_if, r_if]
 
             o.write(("\t").join(outline))
@@ -485,48 +490,49 @@ def print_results(results: dict, outfile: str, vartype: str):
 def main():
     # set up
     args = get_options()
-    inputs = parse_config()
-    mtdir = inputs['matrixtables_lustre_dir']
-    rf_dir = inputs['var_qc_rf_dir']
-    resourcedir = inputs['resource_dir']
-    plot_dir = inputs['plots_dir_local']
+    config = parse_config()
+    mtdir = config['general']['matrixtables_dir']
+    rf_dir = config['general']['var_qc_rf_dir']
+    plot_dir = config['general']['plots_dir']
 
     # initialise hail
-    tmp_dir = "hdfs://spark-master:9820/"
-    sc = pyspark.SparkContext()
+    tmp_dir = config['general']['tmp_dir']
+    sc = pyspark.SparkContext.getOrCreate()
     hadoop_config = sc._jsc.hadoopConfiguration()
-    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38")
+    hl.init(sc=sc, tmp_dir=tmp_dir, default_reference="GRCh38", idempotent=True)
 
-    giab_vcf = resourcedir + "HG001_GRCh38_benchmark.interval.illumina.vcf.gz"
-    giab_cqfile = resourcedir + "all.interval.illumina.vep.info.txt"
+    giab_vcf = path_spark(config['evaluation']['giab_vcf'])
+    giab_cqfile = path_spark(config['evaluation']['giab_cqfile'])
     giab_ht = prepare_giab_ht(giab_vcf, giab_cqfile, mtdir)
 
-    rf_htfile = rf_dir + args.runhash + "/_gnomad_score_binning_tmp.ht"
-    mtfile = mtdir + "mt_varqc_splitmulti.mt"
-    cqfile = resourcedir + "all_consequences.txt"
-    pedfile = "file:///lustre/scratch123/qc/BiB/trios.EGAN.complete.ped"
-    wd = os.path.join(mtdir, args.runhash)
+    rf_htfile = path_spark(os.path.join(rf_dir, args.runhash, "_gnomad_score_binning_tmp.ht"))
+    mtfile = path_spark(config['step3']['split_multi_and_var_qc']['varqc_mtoutfile_split'])
+    cqfile = path_spark(config['step3']['annotate_mt_with_cq_rf_score_and_bin']['cqfile'])
+    pedfile = path_spark(config['step3']['pedfile'])
+    wd = path_spark(os.path.join(mtdir, args.runhash))
 
     mt = hl.read_matrix_table(mtfile)
     mt = clean_mt(mt)
     mt_annot = annotate_with_rf(mt, rf_htfile)
     mt_annot = annotate_cq(mt_annot, cqfile)
 
-    mt_annot_path = os.path.join(wd, 'tmp.hard_filters_combs.mt')
-    # mt_annot.write(mt_annot_path, overwrite=True)
+    mt_annot_path = path_spark(os.path.join(wd, 'tmp.hard_filters_combs.mt'))
+    mt_annot.write(mt_annot_path, overwrite=True)
 
     results = filter_and_count(
         mt_path=mt_annot_path,
         ht_giab=giab_ht,
         pedfile=pedfile,
-        mtdir=wd
+        mtdir=wd,
+        config=config
     )
 
-    outfile_snv = plot_dir + "/" + args.runhash + "_genotype_hard_filter_comparison_snv_5.txt"
-    outfile_indel = plot_dir + "/" + args.runhash + "_genotype_hard_filter_comparison_indel_5.txt"
+    outfile_snv = os.path.join(plot_dir, args.runhash + config['evaluation']['snp_tsv_filesuffix'])
+    outfile_indel = os.path.join(plot_dir, args.runhash + config['evaluation']['indel_tsv_filesuffix'])
     print_results(results, outfile_snv, 'snv')
     print_results(results, outfile_indel, 'indel')
 
 
 if __name__ == '__main__':
+    logging.basicConfig(level=logging.INFO)
     main()
diff --git a/jupyter_notebooks/refactoring/configs.ipynb b/jupyter_notebooks/refactoring/configs.ipynb
new file mode 100644
index 0000000..d4cc12a
--- /dev/null
+++ b/jupyter_notebooks/refactoring/configs.ipynb
@@ -0,0 +1,742 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 258,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_config():\n",
+    "    return {\n",
+    "        'x': 'expanded!',\n",
+    "        'var': {'h':'hello {testvar} expansion'},\n",
+    "        'a': { 'a':1, 'b':2, 'c':3 },\n",
+    "        'b': { 'a':10, 'b':20, 'c':30 },\n",
+    "        'deep': { 'a': {'a':100, 'b':200, 'c':300} },\n",
+    "        'var2': '{testvar} shallow'\n",
+    "    }\n",
+    "\n",
+    "def load_config_alpha(config_obj, *field_names):\n",
+    "    pass"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 259,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(False, True, False, False, True)"
+      ]
+     },
+     "execution_count": 259,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from collections import UserDict\n",
+    "\n",
+    "class MyDict(UserDict):\n",
+    "    pass\n",
+    "\n",
+    "conf = get_config()\n",
+    "a = MyDict(conf)\n",
+    "isinstance(a, dict), isinstance(conf, dict), isinstance(conf, MyDict), isinstance(conf, UserDict), isinstance(a, UserDict)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 260,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from collections import UserDict\n",
+    "\n",
+    "class ConfigSection(UserDict):\n",
+    "    \"\"\"\n",
+    "    A dictionary wrapper that implements some useful features:\n",
+    "    - introspection: a section knows its name and key in the parent section\n",
+    "    - deep (recursive) cast from dict.  \n",
+    "      That is, you can create a Config with Configs from dict with dicts.\n",
+    "    \n",
+    "    Note that isinstance(userDict, dict) == false\n",
+    "    \"\"\"\n",
+    "\n",
+    "    def __init__(self, _dict=None, name=''):\n",
+    "        UserDict.__init__(self, _dict)\n",
+    "\n",
+    "        self.name = name\n",
+    "        \n",
+    "        for key in self.data:\n",
+    "            val = self.data[key]\n",
+    "            if isinstance(val, dict):\n",
+    "                # deep convert dict to config\n",
+    "                if self.name:\n",
+    "                    childname = self.name+'.'+key\n",
+    "                else:\n",
+    "                    childname = key\n",
+    "                self.data[key] = ConfigSection(val, childname)\n",
+    "    \n",
+    "    def getp(self, path: str):\n",
+    "        \"\"\"\n",
+    "        A getter function for dot-separated field paths.\n",
+    "        For instance, `config.getp('a.b.c') == config['a']['b']['c']`.\n",
+    "\n",
+    "        Can return both config sections and values. \n",
+    "        \"\"\"\n",
+    "        keyseq = path.strip('.').split('.')\n",
+    "\n",
+    "        if keyseq[0] not in self.data:\n",
+    "            raise KeyError(f\"ConfigSection '{self.name}' has no '{keyseq[0]}' section\")\n",
+    "\n",
+    "        section = self\n",
+    "        breadcrumbs = self.name\n",
+    "        for nextkey in keyseq:\n",
+    "            if isinstance(section, ConfigSection):\n",
+    "                if nextkey in section:\n",
+    "                    section = section[nextkey]\n",
+    "                    breadcrumbs += '.' + nextkey\n",
+    "                else:\n",
+    "                    raise KeyError(f\"{path} : '{breadcrumbs}' section has no '{nextkey}' field\")\n",
+    "            else:\n",
+    "                raise KeyError(f\"{path} : {breadcrumbs + '.' + nextkey} is a field, not a section\")\n",
+    "        return section\n",
+    "\n",
+    "    def to_flat_dict(self):\n",
+    "        \"\"\"\n",
+    "        Returns a dict with keys in form of 'key1.key2.key3'.\n",
+    "        `section.to_flat_dict()['a.b.c'] == section['a']['b']['c']`\n",
+    "        \"\"\"\n",
+    "        raise NotImplementedError()\n",
+    "\n",
+    "class Config(ConfigSection):\n",
+    "    \"\"\"\n",
+    "    Another dictionary wrapper. Config manages a tree of ConfigSections.\n",
+    "    Features:\n",
+    "    - string variable expansion\n",
+    "    - yaml loading/writing\n",
+    "    \"\"\"\n",
+    "    import re\n",
+    "    \n",
+    "    config_var_def = {\n",
+    "        'tmpdir': 'general.tmp_dir',\n",
+    "        'anndir': 'general.annotation_outdir_local',\n",
+    "        'mtdir': 'general.matrixtables_outdir',\n",
+    "        'testvar': 'x',\n",
+    "    }\n",
+    "\n",
+    "    __path_field_re = re.compile(r\".*_[out|in]?[dir|file]\")\n",
+    "    __cvar_re = re.compile(r\"\\{[a-zA-Z0-9_]+\\}\")\n",
+    "    SKIP_EXPAND = False\n",
+    "    EXPAND_ALL = True\n",
+    "\n",
+    "    @staticmethod\n",
+    "    def _should_expand(fieldname: str):\n",
+    "        return Config.EXPAND_ALL or (\n",
+    "            not Config.SKIP_EXPAND and Config.__path_field_re.fullmatch(fieldname) is not None\n",
+    "        )\n",
+    "\n",
+    "    def _expand_field(self, val: str):\n",
+    "        config_vars = {}\n",
+    "        required_vars = [x[1:-1] for x in Config.__cvar_re.findall(val)]\n",
+    "        for k in required_vars:\n",
+    "            if k in Config.config_var_def:\n",
+    "                config_vars[k] = self.getp(Config.config_var_def[k])\n",
+    "            else:\n",
+    "                config_vars[k] = '{'+k+'}'\n",
+    "        return val.format(**config_vars)\n",
+    "\n",
+    "    def _expand_all_fields(self, section: ConfigSection):\n",
+    "        for key in section.data:\n",
+    "            val = section.data[key]\n",
+    "            if isinstance(val, str) and Config._should_expand(key):\n",
+    "                section.data[key] = self._expand_field(val)\n",
+    "            elif isinstance(val, ConfigSection):\n",
+    "                self._expand_all_fields(val)\n",
+    "\n",
+    "\n",
+    "    def getp(self, path: str):\n",
+    "        \"\"\"\n",
+    "        A getter function for dot-separated field paths.\n",
+    "        For instance, `config.getp('a.b.c') == config['a']['b']['c']`.\n",
+    "\n",
+    "        Can return both config sections and values. \n",
+    "        \"\"\"\n",
+    "        keyseq = path.strip('.').split('.', 1)\n",
+    "        fk = keyseq[0]  # first key\n",
+    "        if fk not in self.data:\n",
+    "            raise KeyError(f\"Config has no '{fk}' section\")\n",
+    "        if len(keyseq) > 1 and not isinstance(self.data[fk], ConfigSection):\n",
+    "            raise KeyError(f\"{path} : {fk} is a field, not a section\")\n",
+    "        if len(keyseq) == 1:\n",
+    "            return self.data[fk]\n",
+    "        remaining_path = keyseq[1]\n",
+    "        return self.data[fk].getp(remaining_path)\n",
+    "\n",
+    "    def __init__(self, _dict=None):\n",
+    "        ConfigSection.__init__(self, _dict, '')\n",
+    "        self._expand_all_fields(self)\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 261,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'x': 'expanded!', 'var': {'h': 'hello expanded! expansion'}, 'a': {'a': 1, 'b': 2, 'c': 3}, 'b': {'a': 10, 'b': 20, 'c': 30}, 'deep': {'a': {'a': 100, 'b': 200, 'c': 300}}, 'var2': 'expanded! shallow'}"
+      ]
+     },
+     "execution_count": 261,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "conf = Config(get_config())\n",
+    "conf"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 262,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "__main__.ConfigSection"
+      ]
+     },
+     "execution_count": 262,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "type(conf.getp('a'))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 263,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'expanded!'"
+      ]
+     },
+     "execution_count": 263,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "conf._expand_field('{testvar}')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 266,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'a': 100, 'b': 200, 'c': 300}"
+      ]
+     },
+     "execution_count": 266,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "conf.getp('deep.a')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "---"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 318,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "def getp(_dict: dict, keypath: str, silent: bool = False, default = None):\n",
+    "    \"\"\"\n",
+    "    Get a value from a tree of dicts using dot-notation. That is, \n",
+    "    `getp(conf, \"a.b.c\") == conf['a']['b']['c']`\n",
+    "\n",
+    "    - `_dict` is a structure of nested dicts\n",
+    "    - `keypath` is a sequence of keys joined by '.'\n",
+    "    - if `silent` then return `default` value on invalid path instead of raising an exception  \n",
+    "\n",
+    "    Note that this function can return a dict as well as a scalar -- it has no output type checks.\n",
+    "    \"\"\"\n",
+    "    keyseq = keypath.strip('.').split('.')\n",
+    "    if keyseq[0] not in _dict:\n",
+    "        if silent: return default\n",
+    "        raise KeyError(f\"top-level dict has no '{keyseq[0]}' key\")\n",
+    "    \n",
+    "    section = _dict\n",
+    "    breadcrumbs = ''\n",
+    "    for nextkey in keyseq:\n",
+    "        if isinstance(section, dict):\n",
+    "            if nextkey in section:\n",
+    "                section = section[nextkey]\n",
+    "                breadcrumbs += '.' + nextkey\n",
+    "            else:\n",
+    "                if silent: return default\n",
+    "                raise KeyError(f\"{keypath} : '{breadcrumbs}' section has no '{nextkey}' field\")\n",
+    "        else:\n",
+    "            if silent: return default\n",
+    "            raise KeyError(f\"{keypath} : {breadcrumbs + '.' + nextkey} is a field, not a section\")\n",
+    "    return section\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 319,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "200"
+      ]
+     },
+     "execution_count": 319,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "\n",
+    "getp(get_config(), 'deep.a.b')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 320,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import re\n",
+    "cvar_re = re.compile(r\"\\{([a-zA-Z0-9_]+(?:\\.[a-zA-Z0-9_]+)*)\\}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 321,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['hello', 'foo.bar']"
+      ]
+     },
+     "execution_count": 321,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "cvar_re.findall('hey{hello}, {foo.bar}/{.omg.hiii}')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "---"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 322,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "def expand_cvars(config: dict, str_with_cvar: str):\n",
+    "    \"\"\"\n",
+    "    Expand config variables in a string.  \n",
+    "    Ignore errors, leave invalid cvars as is.\n",
+    "    \"\"\"\n",
+    "    import re\n",
+    "    # Find all cvars that look like {cvar_name}\n",
+    "    # - no dots at the begininng or at the end\n",
+    "    # - no more 1 dot in a row\n",
+    "    # - a-zA-Z0-9_ as identifiers\n",
+    "    cvar_re = re.compile(r\"\\{([a-zA-Z0-9_]+(?:\\.[a-zA-Z0-9_]+)*)\\}\")\n",
+    "    def repl(cvar_match):\n",
+    "        cvar_name = cvar_match.group(1)\n",
+    "        return str(getp(config, keypath=cvar_name, silent=True, default='{'+cvar_name+'}'))\n",
+    "    expanded_str = cvar_re.sub(repl, str_with_cvar) \n",
+    "    return expanded_str"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 325,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'omg hiii expanded! and 200 and even {do.not.exists}'"
+      ]
+     },
+     "execution_count": 325,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "expand_cvars(get_config(), 'omg hiii {x} and {deep.a.b} and even {do.not.exists}')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "---"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 329,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "def expand_cvars_recursive(config: dict, dict_to_expand, inplace=False):\n",
+    "    \"\"\"\n",
+    "    Recursively expand cvars in all string fields in a nested dict structure `dict_to_expand`\n",
+    "    using data from `config`\n",
+    "    \"\"\"\n",
+    "    if inplace:\n",
+    "        _dict = dict_to_expand\n",
+    "    else:\n",
+    "        from copy import deepcopy\n",
+    "        _dict = deepcopy(dict_to_expand)\n",
+    "    for key in _dict:\n",
+    "        val = _dict[key]\n",
+    "        if isinstance(val, str):\n",
+    "            _dict[key] = expand_cvars(config, val)\n",
+    "        elif isinstance(val, dict):\n",
+    "            expand_cvars_recursive(config, val, inplace=True)\n",
+    "    return _dict\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 330,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'foo': 'hello ten 10 and hundred 100',\n",
+       " 'bar': {'baz': 'hey there from the deep 300',\n",
+       "  'lol': 'shallow this time 30',\n",
+       "  'no': 'no expansion needed',\n",
+       "  'num': 123},\n",
+       " 'num': 456}"
+      ]
+     },
+     "execution_count": 330,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "conf = {\n",
+    "    'a': 10,\n",
+    "    'b': 20,\n",
+    "    'c': 30,\n",
+    "    'deep' : {\n",
+    "        'a': 100,\n",
+    "        'b': 200,\n",
+    "        'c': 300\n",
+    "    }\n",
+    "}\n",
+    "dat = {\n",
+    "    'foo' : 'hello ten {a} and hundred {deep.a}',\n",
+    "    'bar' : {\n",
+    "        'baz': 'hey there from the deep {deep.c}',\n",
+    "        'lol': 'shallow this time {c}',\n",
+    "        'no': 'no expansion needed',\n",
+    "        'num': 123\n",
+    "    },\n",
+    "    'num': 456\n",
+    "}\n",
+    "\n",
+    "expand_cvars_recursive(conf, dat)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 331,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'foo': 'hello ten {a} and hundred {deep.a}',\n",
+       " 'bar': {'baz': 'hey there from the deep {deep.c}',\n",
+       "  'lol': 'shallow this time {c}',\n",
+       "  'no': 'no expansion needed',\n",
+       "  'num': 123},\n",
+       " 'num': 456}"
+      ]
+     },
+     "execution_count": 331,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "dat"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 333,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 333,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "a = expand_cvars_recursive(conf, dat, inplace=True)\n",
+    "a == dat"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 334,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'foo': 'hello ten 10 and hundred 100',\n",
+       " 'bar': {'baz': 'hey there from the deep 300',\n",
+       "  'lol': 'shallow this time 30',\n",
+       "  'no': 'no expansion needed',\n",
+       "  'num': 123},\n",
+       " 'num': 456}"
+      ]
+     },
+     "execution_count": 334,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "a"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "---"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 364,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "__is_path_field_re = re.compile(r\"(out|in)?(dir|file)(_local)?$\")\n",
+    "\n",
+    "def is_path_field(fieldname):\n",
+    "    return __is_path_field_re.search(fieldname) is not None"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 363,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "('out', 'dir', '_local')"
+      ]
+     },
+     "execution_count": 363,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "__is_path_field_re.search('test.fii.asd.resource_outdir_local').groups()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "---"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 365,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "path_cvar_re = re.compile(r\"(\\/|\\\\)?\\{([a-zA-Z0-9_]+(?:\\.[a-zA-Z0-9_]+)*)\\}(\\/|\\\\)?\")\n",
+    "pr = 'foo/{r}'\n",
+    "pl = '{l}/bar'\n",
+    "plr = 'foo/{lr}/bar'\n",
+    "\n",
+    "conf = {\n",
+    "    'l': '/leftdir/',\n",
+    "    'r': '/rightdir',\n",
+    "    'rl': '/middledir/',\n",
+    "}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 371,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "('/', 'lr', '/')"
+      ]
+     },
+     "execution_count": 371,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "path_cvar_re.search(plr).groups()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 391,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "('file:', 'usr', 'plots', 'plot.1.jpg')"
+      ]
+     },
+     "execution_count": 391,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import pathlib\n",
+    "path_with_cvars = pathlib.Path('file:///usr/plots//plot.1.jpg')\n",
+    "path_with_cvars.parts"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 392,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'file:/usr/plots/plot.1.jpg'"
+      ]
+     },
+     "execution_count": 392,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import posixpath \n",
+    "posixpath.normpath('file:///usr/plots//plot.1.jpg')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 403,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "7"
+      ]
+     },
+     "execution_count": 403,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "protocol_re = re.compile(r\"[a-zA-Z][a-zA-Z0-9]*:\\/\\/\")\n",
+    "protocol_needed = protocol_re.match('file:///usr/plots//plot.1.jpg')\n",
+    "protocol_needed.end()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "fastlbp",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.19"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/run_all_steps.sh b/run_all_steps.sh
new file mode 100644
index 0000000..158e06b
--- /dev/null
+++ b/run_all_steps.sh
@@ -0,0 +1,38 @@
+#!/bin/bash
+
+# Set up
+export PYTHONPATH=$(pwd)
+export WES_CONFIG=$(pwd)/config/new_config_example.yaml
+echo "Using config ${WES_CONFIG}"
+
+
+# Step 1
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 1-import_data/1-import_gatk_vcfs_to_hail.py
+
+# Step 2
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 2-sample_qc/1-hard_filters_sex_annotation.py
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 2-sample_qc/2-prune_related_samples.py
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 2-sample_qc/3-population_pca_prediction.py --kg_to_mt
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 2-sample_qc/3-population_pca_prediction.py --run
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 2-sample_qc/4-find_population_outliers.py
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 2-sample_qc/5-filter_fail_sample_qc.py
+
+# Step 3
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 3-variant_qc/variant_qc_non_trios/1-generate_truth_sets_non_trios.py --all
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 3-variant_qc/variant_qc_non_trios/2-create_rf_ht_non_trios.py
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit --master local[*] 3-variant_qc/3-train_rf.py --manual_runhash controllable_test_run_id
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit --master local[*] 3-variant_qc/4-apply_rf.py --runhash controllable_test_run_id
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 3-variant_qc/variant_qc_non_trios/5-annotate_ht_after_rf_no_trios.py --runhash controllable_test_run_id
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 3-variant_qc/variant_qc_non_trios/6-rank_and_bin_no_trios.py --runhash controllable_test_run_id
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 3-variant_qc/variant_qc_non_trios/7-plot_rf_output_no_trios.py --runhash controllable_test_run_id
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 3-variant_qc/8-select_thresholds.py --runhash controllable_test_run_id --snv 92 --indel 68
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 3-variant_qc/9-filter_mt_after_variant_qc.py --runhash controllable_test_run_id --snv 84 --indel 60
+
+# Step 4
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 4-genotype_qc/1-apply_hard_filters.py --dp 5 --gq 10 --ab 0.2
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 4-genotype_qc/1a-apply_range_of_hard_filters.py --runhash controllable_test_run_id
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 4-genotype_qc/2-counts_per_sample.py
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 4-genotype_qc/3-export_vcfs.py
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 4-genotype_qc/3a-export_vcfs_range_of_hard_filters.py --runhash controllable_test_run_id
+PYSPARK_DRIVER_PYTHON=/home/ubuntu/venv/bin/python spark-submit 4-genotype_qc/3b-export_vcfs_stingent_filters.py --runhash controllable_test_run_id
+
diff --git a/tests/README.md b/tests/README.md
new file mode 100644
index 0000000..1a3befa
--- /dev/null
+++ b/tests/README.md
@@ -0,0 +1,30 @@
+# How to run tests
+
+## Unit tests
+
+Run all tests with: 
+```Python
+cd unit_tests/
+python -m unittest test_all_modules
+```
+
+To run individual tests, you have to specify the test name. For instance:
+```Python
+python -m unittest test_all_modules.TestQCSteps.test_1_1_load_vcfs_to_mt
+```
+
+Unit tests can be executed in any order as they rely on reference test data stored in the S3 storage.
+
+## Integration tests
+Similarly to the unit tests, run all integration tests with:
+```Python
+cd integration_tests
+python -m unittest test_integrations
+```
+
+Or select specific tests to run:
+```Python
+python -m unittest test_integrations.IntegrationTests.test_1_1_import_data
+```
+> [!NOTE]
+> Integration tests test the whole pipeline steps for possible errors. Since some steps of the QC require the outputs of the previous steps, the execution order of the tests matters. Make sure to run the whole integration test suite first to get all the necessary files generated. Alternatively, you can opt for running separate tests, but keep in mind that this would require having all the inputs required by the tested step. 
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/config_tests/sample-config.yaml b/tests/config_tests/sample-config.yaml
new file mode 100644
index 0000000..5951702
--- /dev/null
+++ b/tests/config_tests/sample-config.yaml
@@ -0,0 +1,50 @@
+# Sample config to test config parser
+# - cvar_custom should point to group_0.not_cvar
+
+cvars:
+  cvar_3: group_0.not_cvar
+
+cvar_1: /dev/null/
+
+group_0:
+  # CVAR cvar_3
+  not_cvar: /lorem/ipsum/
+
+group_1:
+  cvar_2: /foo/bar/
+
+group_2:
+  # should become /dev/null/baz.baz
+  f1_file: '{cvar_1}/baz.baz'
+  # should become /foo/bar/baz.baz
+  f2_file: '{group_1.cvar_2}/baz.baz'
+  # should become /lorem/ipsum/baz.baz
+  f3_file: '{cvar_3}/baz.baz'
+  # should become /lorem/ipsum/baz.baz
+  f4_file: '{cvar_custom}/baz.baz'
+
+  subgroup:
+    # should become /dev/null/baz.baz
+    f1_file: '{cvar_1}/baz.baz'
+    # should become /foo/bar/baz.baz
+    f2_file: '{group_1.cvar_2}/baz.baz'
+    # should become /lorem/ipsum/baz.baz
+    f3_file: '{cvar_3}/baz.baz'
+    # should become /lorem/ipsum/baz.baz
+    f4_file: '{cvar_custom}/baz.baz'
+
+  a1: 100.0
+
+# should remain empty
+empty_file: ''
+
+# recurrent substitution test
+# misc substitution tests
+group_3:
+  subgroup:
+    f1: '12345'
+    f2: '{group_3.subgroup.f1}_1' # -> 12345_1
+    f3: '{group_3.subgroup.f2}2' # -> 12345_12
+  f4: '{group_3.subgroup.f3}3' # -> 12345_123
+  f5: '{group_3.f4}4' # -> 12345_1234
+  f1_1: '{group_3.subgroup.f2}x{group_3.f4}' # -> 12345_1x12345_123
diff --git a/tests/config_tests/test_config_parser.py b/tests/config_tests/test_config_parser.py
new file mode 100644
index 0000000..454e649
--- /dev/null
+++ b/tests/config_tests/test_config_parser.py
@@ -0,0 +1,182 @@
+from utils.config import parse_config, parse_config_file, getp, parent_section, is_subsection, flatten, flat_to_nested, resolve_cvar_flat
+from pathlib import PurePath
+import unittest
+import os
+
+class TestConfigParser(unittest.TestCase):
+
+    def test_parent_section(self):
+        self.assertEqual(parent_section(''), '')
+        self.assertEqual(parent_section('.'), '')
+        self.assertEqual(parent_section('a'), '')
+        self.assertEqual(parent_section('contra-spem-spero'), '')
+        self.assertEqual(parent_section('a.b'), 'a')
+        self.assertEqual(parent_section('contra-spem-spero.b'), 'contra-spem-spero')
+        self.assertEqual(parent_section('a.b.c'), 'a.b')
+        self.assertEqual(parent_section('contra.spem.spero'), 'contra.spem')
+
+    def test_subsections(self):
+        self.assertTrue(is_subsection('', ''))
+        self.assertTrue(is_subsection('a', ''))
+        self.assertTrue(is_subsection('contra-spem-spero', ''))
+        self.assertTrue(is_subsection('a.b', 'a'))
+        self.assertTrue(is_subsection('contra-spem-spero.b', 'contra-spem-spero'))
+        self.assertTrue(is_subsection('a.b.c', 'a.b'))
+        self.assertTrue(is_subsection('contra.spem.spero', 'contra.spem'))
+        self.assertFalse(is_subsection('', 'a'))
+        self.assertFalse(is_subsection('', 'contra-spem-spero'))
+        self.assertFalse(is_subsection('a', 'a.b'))
+        self.assertFalse(is_subsection('contra-spem-spero', 'contra-spem-spero.b'))
+        self.assertFalse(is_subsection('a.b', 'a.b.c'))
+        self.assertFalse(is_subsection('contra.spem', 'contra.spem.spero'))
+
+    def test_flatten(self):
+        d = {
+            'a': {
+                'b': 'a.b',
+                'c': 'a.c',
+                'd': { 'e': 'a.d.e', 'i1': 100 },
+                'i2': 200,
+                'f': { 'e': 'a.f.e', 'i4': 400 },
+                'empty': dict()
+            },
+            'L1': [10, 20, 30],
+            'L2': ['xx','yy','zz'],
+            'b': dict(),
+            'i3': 300
+        }
+        expected_d = {
+            'a.b': 'a.b',
+            'a.c': 'a.c',
+            'a.d.e': 'a.d.e',
+            'a.d.i1': 100,
+            'a.i2': 200,
+            'a.f.e': 'a.f.e',
+            'a.f.i4': 400,
+            # 'a.empty': dict(), # should not be added
+            'L1': [10, 20, 30],
+            'L2': ['xx','yy','zz'],
+            # 'b': dict(), # should not be added
+            'i3': 300
+        }
+        
+        flat_d = flatten(d)
+        
+        self.assertDictEqual(expected_d, flat_d)
+        
+        # Order is important as well
+        self.assertTupleEqual(tuple(expected_d.keys()), tuple(flat_d.keys()), "Order is wrong")
+
+        # Change order
+        expected_d.pop('a.b')
+        expected_d['a.b'] = 'a.b'
+        self.assertFalse(tuple(expected_d.keys()) == tuple(flat_d.keys()))
+
+    def test_flat_to_nested(self):
+        flat_d = {
+            'a.b': 'a.b',
+            'a.c': 'a.c',
+            'a.d.e': 'a.d.e',
+            'a.d.i1': 100,
+            'a.i2': 200,
+            'a.f.e': 'a.f.e',
+            'a.f.i4': 400,
+            # 'a.empty': dict(), # should not be added
+            'L1': [10, 20, 30],
+            'L2': ['xx','yy','zz'],
+            # 'b': dict(), # should not be added
+            'i3': 300
+        }
+        d = flat_to_nested(flat_d)
+        flat_again_d = flatten(d, separator='$')
+        expected_flat_again_d = { key.replace('.','$'): val for key,val in flat_d.items() }
+
+        # Idempotence. Basically, flat_d == flatten(flat_to_nested(flat_d)).
+        # Insertion/iteration order is important as well.
+        self.assertTupleEqual(tuple(expected_flat_again_d.items()), tuple(flat_again_d.items()))
+
+        # Ensure the dict is really nested
+        self.assertEqual(d['a']['b'], 'a.b')
+        self.assertEqual(d['a']['d']['e'], 'a.d.e')
+        self.assertEqual(d['a']['d']['i1'], 100) # ensure types are ok
+
+    def test_resolve_cvar(self):
+        config = {
+            'cvars.cvar0': 'a.x',
+            'cvars.cvar1': 'x',
+            'x': 'toplevel',
+            'a.x': 'axxxx',
+            'a.y': 'ayyyy',
+            'b': '{cvar0}'
+        }
+
+        # config is FLAT on purpose
+        self.assertEqual(resolve_cvar_flat('cvar0', config, 'field', True), 'axxxx') # cvar shortcut
+        self.assertEqual(resolve_cvar_flat('a.x', config, 'field', True), 'axxxx') # full key
+        self.assertEqual(resolve_cvar_flat('x', config, 'field', True), 'toplevel') # full key
+        self.assertEqual(resolve_cvar_flat('x', config, 'a.other', True), 'axxxx') # local key in section a
+        self.assertEqual(resolve_cvar_flat('.x', config, 'a.other', True), 'toplevel') # explicit full key / absolute key
+        self.assertEqual(resolve_cvar_flat('cvar1', config, 'a.other', True), 'toplevel') # cvar shortcut points to the full key
+        self.assertEqual(resolve_cvar_flat('a.nonexistant', config, '', True), '{a.nonexistant}')
+        self.assertEqual(resolve_cvar_flat('a.nonexistant.nonexistant', config, '', True), '{a.nonexistant.nonexistant}')
+
+
+    def test_cvars(self):
+        expected_config = {
+            'cvars.cvar_3': 'group_0.not_cvar',
+            'cvars.cvar_custom': 'group_0.not_cvar', # This should be the second one, as custom cvars are inserted in the end, 
+                                                     # and we are doing a depth-first iteration
+            'cvar_1': '/dev/null/',
+            'group_0.not_cvar': '/lorem/ipsum/',
+            'group_1.cvar_2': '/foo/bar/',
+            'group_2.f1_file': str(PurePath('/dev/null/baz.baz')),
+            'group_2.f2_file': str(PurePath('/foo/bar/baz.baz')),
+            'group_2.f3_file': str(PurePath('/lorem/ipsum/baz.baz')),
+            'group_2.f4_file': str(PurePath('/lorem/ipsum/baz.baz')),
+            'group_2.subgroup.f1_file': str(PurePath('/dev/null/baz.baz')),
+            'group_2.subgroup.f2_file': str(PurePath('/foo/bar/baz.baz')),
+            'group_2.subgroup.f3_file': str(PurePath('/lorem/ipsum/baz.baz')),
+            'group_2.subgroup.f4_file': str(PurePath('/lorem/ipsum/baz.baz')),
+            'group_2.a1': 100.0,
+            'empty_file': '',
+            'group_3.subgroup.f1': '12345',
+            'group_3.subgroup.f2': '12345_1',
+            'group_3.subgroup.f3': '12345_12',
+            'group_3.f4': '12345_123',
+            'group_3.f5': '12345_1234',
+            'group_3.f1_1': '12345_1x12345_123',
+        }
+        config = parse_config('tests/config_tests/sample-config.yaml', { 'cvar_custom': 'group_0.not_cvar' })
+        # print(config)        
+        flat_config = flatten(config)
+        self.assertTupleEqual(tuple(expected_config.items()), tuple(flat_config.items()))
+        
+        # ensure config is NESTED and not FLAT
+        self.assertEqual(config['group_1']['cvar_2'], expected_config['group_1.cvar_2'])
+        self.assertEqual(config['group_2']['f1_file'], expected_config['group_2.f1_file'])
+        self.assertEqual(config['group_3']['subgroup']['f3'], expected_config['group_3.subgroup.f3'])
+
+        # Test the whole file loading process
+
+        os.environ['WES_CONFIG'] = os.path.abspath('tests/config_tests/sample-config.yaml')
+        config = parse_config(additional_cvar_shortcuts={ 'cvar_custom': 'group_0.not_cvar' })
+        flat_config = flatten(config)
+        self.assertTupleEqual(tuple(expected_config.items()), tuple(flat_config.items()))
+
+        # ensure config is NESTED and not FLAT
+        self.assertEqual(config['group_1']['cvar_2'], expected_config['group_1.cvar_2'])
+        self.assertEqual(config['group_2']['f1_file'], expected_config['group_2.f1_file'])
+        self.assertEqual(config['group_3']['subgroup']['f3'], expected_config['group_3.subgroup.f3'])
+
+
+    # TODO
+    def test_undefined_cvar(self):
+        with self.assertRaisesRegex(
+            ValueError, 
+            "cannot substitute undefined config variable 'b' referenced in field 'a'" 
+            ) as cm:
+            config = parse_config('tests/config_tests/undefined-cvar-config.yaml')
+
+if __name__ == '__main__':
+    unittest.main()
+
diff --git a/tests/config_tests/undefined-cvar-config.yaml b/tests/config_tests/undefined-cvar-config.yaml
new file mode 100644
index 0000000..2e91601
--- /dev/null
+++ b/tests/config_tests/undefined-cvar-config.yaml
@@ -0,0 +1,5 @@
+# Sample config to test config parser.
+# This config should raise an exception
+
+a: '{b}'
+b: 'foo'
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diff --git a/tests/integration_tests/__init__.py b/tests/integration_tests/__init__.py
new file mode 100644
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diff --git a/tests/integration_tests/inputs_test_template.yaml b/tests/integration_tests/inputs_test_template.yaml
new file mode 100644
index 0000000..4a20061
--- /dev/null
+++ b/tests/integration_tests/inputs_test_template.yaml
@@ -0,0 +1,65 @@
+---
+
+# hail setup parameter
+tmp_dir: file://{INTEGRATION_TESTS_DIR}/tmp
+
+# --- Step 1.1 --- #
+# gatk_vcf_header: file://{INTEGRATION_TESTS_DIR}/gatk_vcf_header.txt # TODO: make optional
+gatk_import_lustre_dir: file://{TEST_DATA_DIR} # test with the small dataset
+load_matrixtables_lustre_dir: {INTEGRATION_TESTS_DIR}/matrixtables/ # not used in this step
+# matrixtables_lustre_dir: file://{INTEGRATION_TESTS_DIR}/matrixtables/ # used in this step 
+
+# --- Step 2.1 --- #
+#load_matrixtables_lustre_dir: /lustre/scratch126/dh24_test/qc_test/matrixtables/mts_for_control_datasets/
+annotation_lustre_dir: file://{INTEGRATION_TESTS_DIR}/annotations/
+annotation_lustre_dir_local: {INTEGRATION_TESTS_DIR}/annotations/ # TODO: clarify the purpose of these _local duplicates, not used in this step
+matrixtables_lustre_dir: file://{INTEGRATION_TESTS_DIR}/matrixtables/
+resource_dir: file://{RESOURCES_DIR}
+
+# --- Step 2.2 --- #
+#matrixtables_lustre_dir: file:///lustre/scratch126/dh24_test/qc_test/matrixtables/mts_for_control_datasets/
+plots_lustre_dir: file://{INTEGRATION_TESTS_DIR}/plots/ # TODO: not used?
+plots_dir_local: {INTEGRATION_TESTS_DIR}/plots/
+# resource_dir: file://{INTEGRATION_TESTS_DIR}/resources/
+resource_dir_local: {INTEGRATION_TESTS_DIR}/resources/
+training_set_dir: file://{INTEGRATION_TESTS_DIR}/training_sets/
+var_qc_rf_dir: file://{INTEGRATION_TESTS_DIR}/variant_qc_random_forest/
+vcf_output_dir: file://{INTEGRATION_TESTS_DIR}/filtered_vcfs/
+
+rf_test_interval: chr20
+
+#hard filter
+hard_filters:
+  missingness: 0.5
+  snp:
+    relaxed:
+      bin: 92
+      dp: 5
+      gq: 10
+      ab: 0.2
+    medium:
+      bin: 88
+      dp: 5
+      gq: 10
+      ab: 0.2
+    stringent:
+      bin: 84
+      dp: 5
+      gq: 15
+      ab: 0.2
+  indel:
+    relaxed:
+      bin: 68
+      dp: 5
+      gq: 10
+      ab: 0.2
+    medium:
+      bin: 66
+      dp: 5
+      gq: 15
+      ab: 0.2
+    stringent:
+      bin: 58
+      dp: 5
+      gq: 20
+      ab: 0.3
diff --git a/tests/integration_tests/new_config_test_template.yaml b/tests/integration_tests/new_config_test_template.yaml
new file mode 100644
index 0000000..f2b19c0
--- /dev/null
+++ b/tests/integration_tests/new_config_test_template.yaml
@@ -0,0 +1,354 @@
+---
+
+cvars:
+  tmpdir: general.tmp_dir
+  anndir: general.annotation_dir
+  mtdir: general.matrixtables_dir
+  resdir: general.resource_dir
+  1kg_resdir: general.onekg_resource_dir
+  pltdir: general.plots_dir
+  traindir: general.training_sets_dir
+  rfdir: general.var_qc_rf_dir
+
+general:
+  # CVAR tmpdir
+  tmp_dir: {INTEGRATION_TESTS_DIR}/tmp_new_config/ # output
+
+  # CVAR anndir
+  annotation_dir: {INTEGRATION_TESTS_DIR}/annotations_new_config/ # output
+  
+  # CVAR mtdir
+  matrixtables_dir: {INTEGRATION_TESTS_DIR}/matrixtables_new_config/ # output
+
+  # CVAR resdir
+  resource_dir: {RESOURCES_DIR} # input and output
+
+  # CVAR 1kg resource dir
+  onekg_resource_dir: {RESOURCES_DIR}/mini_1000G # input; must be without trailing slash (TODO: make more robust)
+
+  # CVAR pltdir
+  plots_dir: {INTEGRATION_TESTS_DIR}/plots_new_config/ # output
+
+  # CVAR traindir
+  training_sets_dir: {TRAINING_SETS_DIR} # input
+
+  # CVAR rfdir
+  var_qc_rf_dir: {VARIANT_QC_RANDOM_FOREST_DIR} # output 
+
+step1:
+  # --- Step 1.1 --- #
+  gatk_vcf_header_infile:
+  gatk_vcf_indir: {TEST_DATA_DIR}
+  gatk_mt_outfile: '{mtdir}/gatk_unprocessed.mt'
+
+
+step2:
+  # --- Step 2.1 --- #
+  sex_annotation_hard_filters:
+    filtered_mt_outfile: '{mtdir}/mt_hard_filters_annotated.mt'
+    n_alt_alleles_threshold: 0.001
+    defined_gt_frac_threshold: 0.99
+
+  impute_sex:
+    sex_ht_outfile: '{anndir}/sex_annotated.sex_check.txt.bgz'
+    sex_mt_outfile: '{mtdir}/mt_sex_annotated.mt'
+    female_threshold: 0.5
+    male_threshold: 0.8
+    aaf_threshold: 0.05
+    
+  sex_inconsistencies:
+    sex_metadata_file: '{resdir}/mlwh_sample_and_sex.txt'
+    conflicting_sex_report_file: '{anndir}/conflicting_sex.txt.bgz' # output
+    fstat_outliers_report_file: '{anndir}/sex_annotation_f_stat_outliers.txt.bgz' # output
+    fstat_low: 0.2
+    fstat_high: 0.8
+
+  # --- Step 2.2 --- #
+  prune:
+    pruned_mt_file: '{mtdir}/mt_ldpruned.mt' # output
+    ld_prune_args:
+      r2: 0.2
+      # bp_window_size:
+      # memory_per_core:
+      # keep_higher_maf:
+      # block_size: 
+
+  # for function `pc_relate()`
+  prune_pc_relate:
+    relatedness_ht_file: '{mtdir}/mt_relatedness.ht' # output 
+    samples_to_remove_file: '{mtdir}/mt_related_samples_to_remove.ht' # output
+    scores_file: '{mtdir}/mt_pruned.pca_scores.ht' # output
+    pca_components: 3
+    pc_relate_args:
+      min_individual_maf: 0.05
+      block_size: 4096
+      min_kinship: 0.05
+      statistics: 'kin2'
+      # k:
+      # include_self_kinship:
+    relatedness_column: 'kin'
+    relatedness_threshold: 0.125
+    
+  # for function `population_pca()`
+  prune_plot_pca:
+    plink_outfile: '{mtdir}/mt_unrelated.plink'
+    pca_components: 4
+    pca_scores_file: '{mtdir}/mt_pca_scores.ht' # output
+    pca_loadings_file: '{mtdir}/mt_pca_loadings.ht' # output
+    pca_mt_file: '{mtdir}/mt_pca.mt' # output
+    plot_outfile: '{pltdir}/pca.html' # output
+  
+  # --- Step 2.3 --- #
+  create_1kg_mt:
+    indir: '{1kg_resdir}'
+    vcfheader: '{1kg_resdir}/header_20201028.txt' # not available for the test data, this parameter is ignored
+    mt_out_file: '{mtdir}/kg_wes_regions.mt' # output
+
+  merge_with_1_kg:
+    kg_mt_file: '{mtdir}/kg_wes_regions.mt'
+    merged_mt_outfile: '{mtdir}/merged_with_1kg.mt' # output
+
+  annotate_and_filter:
+    pops_file: '{resdir}/igsr_samples.tsv'
+    call_rate: 0.99
+    AF: 0.05
+    p_value_hwe: 0.00005
+    long_range_ld_file: '{resdir}/long_ld_regions.hg38.bed'
+    filtered_mt_outfile: '{mtdir}/merged_with_1kg_filtered.mt'
+  
+  run_pca:
+    pca_scores_outfile: '{mtdir}/pca_scores_after_pruning.ht'
+    pca_loadings_outfile: '{mtdir}/pca_loadings_after_pruning.ht'
+    pca_evals_outfile: '{mtdir}/pca_evals_after_pruning.txt'
+
+  predict_pops:
+    pca_scores_file: '{mtdir}/pca_scores_after_pruning.ht'
+    gnomad_pc_n_estimators: 100
+    gnomad_prop_train: 0.8
+    gnomad_min_prob: 0.5
+    pop_ht_outfile: '{mtdir}/pop_assignments.ht'
+    pop_ht_outtsv: '{mtdir}/pop_assignments.tsv'
+
+  # --- Step 2.4 --- #
+  # func name: annotate_mt
+  annotate_with_pop:
+    annotated_mt_file: '{mtdir}/gatk_unprocessed_with_pop.mt' # output
+
+  stratified_sample_qc:
+    mt_qc_outfile: '{mtdir}/mt_pops_sampleqc.mt' # output
+    ht_qc_cols_outfile: '{mtdir}/mt_pops_sampleqc.ht' # output
+    qc_filter_file: '{mtdir}/mt_pops_QC_filters.ht' # output
+
+    min_depth: 20
+    min_genotype_quality: 20
+    min_vaf: 0.25
+    output_text_file: '{anndir}/sample_qc_by_pop.tsv.bgz' # output
+    output_globals_json_file: '{anndir}/sample_qc_by_pop.globals.json' # output
+  
+  # --- Step 2.5 --- #
+  remove_sample_qc_fails:
+    samples_failing_qc_file: '{anndir}/samples_failing_qc.tsv.bgz' # output
+    sample_qc_filtered_mt_file: '{mtdir}/mt_pops_QC_filters_after_sample_qc.mt' # output
+
+
+step3:
+  # Parameters used in multiple functions # 
+  pedfile: '{resdir}/trios.EGAN.complete.ped'
+
+  # --- Step 3.1 --- #
+  get_truth_ht:
+    truth_ht_outfile: '{resdir}/truthset_table.ht'
+    omni: '{traindir}/1000G_omni2.5.hg38.ht'
+    mills: '{traindir}/Mills_and_1000G_gold_standard.indels.hg38.ht'
+    thousand_genomes: '{traindir}/1000G_phase1.snps.high_confidence.hg38.ht' 
+    hapmap: '{traindir}/hapmap_3.3.hg38.ht'
+
+  split_multi_and_var_qc:
+    mtfile: '{mtdir}/mt_pops_QC_filters_after_sample_qc.mt' # gatk_broad_crams_sanger_calls.mt for non-trios mode
+    varqc_mtoutfile: '{mtdir}/mt_varqc.mt'
+    varqc_mtoutfile_split: '{mtdir}/mt_varqc_splitmulti.mt'
+
+  pedfile: '{resdir}/trios.EGAN.complete.ped'
+
+  # not used for non-trios mode
+  trio_family_dnm_annotation:
+    trio_mtoutfile: '{mtdir}/trios.mt'
+    trio_stats_htoutfile: '{mtdir}/trio_stats.ht'
+    fam_stats_htoutfile: '{mtdir}/family_stats.ht'
+    fam_stats_mtoutfile: '{mtdir}/family_stats.mt'
+    fam_stats_gnomad_mtoutfile: '{mtdir}/family_stats_gnomad.mt'
+    gnomad_htfile: '{resdir}/gnomad.exomes.r2.1.1.sites.liftover_grch38.ht'
+    dnm_htoutfile: '{mtdir}/denovo_table.ht'
+
+  create_inbreeding_ht_with_ac_and_allele_data:
+    inbreeding_htoutfile: '{mtdir}/inbreeding.ht'
+    qc_ac_htoutfile: '{mtdir}/qc_ac.ht'
+    allele_data_htoutfile: '{mtdir}/allele_data.ht'
+
+  # --- Step 3.2 --- #
+  create_rf_ht:
+    fail_hard_filters_QD_less_than: 2
+    fail_hard_filters_FS_greater_than: 60
+    fail_hard_filters_MQ_less_than: 30
+
+    truthset_file: '{resdir}/truthset_table.ht'
+    trio_stats_file: '{mtdir}/trio_stats.ht'
+    allele_data_file: '{mtdir}/allele_data.ht'
+    allele_counts_file: '{mtdir}/qc_ac.ht'
+    inbreeding_file: '{mtdir}/inbreeding.ht'
+    mtfile: '{mtdir}/mt_varqc_splitmulti.mt'
+    htoutfile_rf_all_cols: '{mtdir}/ht_for_RF_all_cols.ht'
+    htoutfile_rf_var_type_all_cols: '{mtdir}/ht_for_RF_by_variant_type_all_cols.ht'
+
+  # --- Step 3.3 --- #
+  rf_test_interval: chr20 # used in multiple functions
+  runs_json: '{rfdir}/rf_runs.json'
+
+  train_rf:
+    input_ht_file: '{mtdir}/ht_for_RF_by_variant_type_all_cols.ht'
+    gnomad_train_rf_fp_to_tp: 1.0
+    gnomad_train_rf_num_trees: 500
+    gnomad_train_rf_max_depth: 5
+
+
+  # --- Step 3.4 --- #
+  # only var_qc_rf_dir (CVAR) is needed
+
+
+  # --- Step 3.5 --- #
+  add_cq_annotation:
+    synonymous_file: '{resdir}/synonymous_variants.txt'
+
+  dnm_and_family_annotation:
+    dnm_htfile: '{mtdir}/denovo_table.ht'
+    fam_stats_htfile: '{mtdir}/family_stats.ht'
+    trio_stats_htfile: '{mtdir}/trio_stats.ht'
+
+  transmitted_singleton_annotation:
+    trio_mtfile: '{mtdir}/trios.mt'
+    trio_filtered_mtfile: '{mtdir}/trios_filtered_.mt'
+
+  annotate_gnomad:
+    gnomad_htfile: '{resdir}/gnomad.exomes.r2.1.1.sites.liftover_grch38.ht'
+
+  
+  # --- Step 3.6 --- #
+  add_rank:
+    subrank_expr_de_novo_high_quality_rank: 0.9
+    subrank_expr_de_novo_medium_quality_rank: 0.5
+
+  create_binned_data_initial:
+    truth_htfile: '{resdir}/truthset_table.ht'
+
+    high_quality_p_de_novo: 0.99
+    medium_quality_p_de_novo: 0.5
+
+    n_trans_common_gnomad_af: 0.1
+    n_untrans_common_gnomad_af: 0.1
+
+
+  # --- Step 3.7 --- #
+  create_plots:
+    qc_plots_settings:
+      mean_point_size: 4.0
+      min_point_size: 1.0
+      max_point_size: 16.0
+      label_text_font_size: "14pt"
+      title_text_font_size: "16pt"
+      subtitle_text_font_size: "14pt"
+      axis_axis_label_text_font_size: "16pt"
+      axis_axis_label_text_font_style: "normal"
+      axis_major_label_text_font_size: "14pt"
+
+
+  # --- Step 3.8 --- #
+  # no config parameters used
+
+  # --- Step 3.9 --- #
+  annotate_mt_with_cq_rf_score_and_bin:
+    mtfile: '{mtdir}/mt_varqc_splitmulti.mt'
+    cqfile: '{resdir}/all_consequences.txt'
+    mtoutfile_after_varqc: '{mtdir}/mt_after_var_qc.mt'
+
+step4:
+  # --- Step 4.1 --- #
+  filter_mt:
+    mtfile: '{mtdir}/mt_after_var_qc.mt'
+    mtoutfile_filtered: '{mtdir}/mt_after_var_qc_hard_filter_gt.mt'
+
+  # --- Step 4.1a --- #
+
+  annotate_cq_rf:
+    mtfile: '{mtdir}/mt_varqc_splitmulti.mt'
+    cqfile: '{resdir}/all_consequences_with_gene_and_csq.txt'
+
+  apply_hard_filters:
+    hard_filters:
+      missingness: 0.5
+      snp:
+        relaxed:
+          bin: 92
+          dp: 5
+          gq: 10
+          ab: 0.2
+        medium:
+          bin: 88
+          dp: 5
+          gq: 10
+          ab: 0.2
+        stringent:
+          bin: 84
+          dp: 5
+          gq: 15
+          ab: 0.2
+      indel:
+        relaxed:
+          bin: 68
+          dp: 5
+          gq: 10
+          ab: 0.2
+        medium:
+          bin: 66
+          dp: 5
+          gq: 15
+          ab: 0.2
+        stringent:
+          bin: 58
+          dp: 5
+          gq: 20
+          ab: 0.3
+
+  # used as an output of the whole step
+  mtoutfile_annot: '{mtdir}/mt_hard_filter_combinations.mt'
+
+  # --- Step 4.2 --- #
+  annotate_gnomad:
+    # mtfile: '{mtdir}/mt_after_var_qc_hard_filter_gt.mt' # used when 1-apply_hard_filters is run
+    mtfile: '{mtdir}/mt_hard_filter_combinations.mt' # used when 1a-apply_hard_filters is run
+    gnomad_htfile: '{resdir}/gnomad.exomes.r2.1.1.sites.liftover_grch38.ht'
+
+  get_trans_untrans_synon_singleton_counts:
+    pedfile: '{resdir}/trios.ped'
+
+  get_counts_per_cq:
+    cqfile: '{pltdir}/variant_counts_per_cq_post_qc.txt'
+  
+  get_ca_fractions:
+    cafile: '{pltdir}/frac_ca_per_sample_post_qc_snv.txt'
+
+  # --- Step 4.3 --- #
+  export_vcfs:
+    mtfile_filtered: '{mtdir}/mt_after_var_qc_hard_filter_gt.mt'
+    vcf_output_dir: '{INTEGRATION_TESTS_DIR}/filtered_vcfs/' 
+
+  # --- Step 4.3a --- #
+
+  # using vcf_output_dir from the previous step
+  export_vcfs_a:
+    mtfile: '{mtdir}/mt_hard_filter_combinations.mt'
+    vcf_output_dir: '{INTEGRATION_TESTS_DIR}/filtered_vcfs_combinations/'
+
+  # --- Ster 4.3b --- #
+  export_vcfs_b:
+    mtfile: '{mtdir}/mt_hard_filter_combinations.mt'
+    filtered_vcf_dir: '{INTEGRATION_TESTS_DIR}/filtered_vcfs_combinations_stringent/'  
diff --git a/tests/integration_tests/test_integrations.py b/tests/integration_tests/test_integrations.py
new file mode 100644
index 0000000..5cf49a8
--- /dev/null
+++ b/tests/integration_tests/test_integrations.py
@@ -0,0 +1,282 @@
+import os
+import argparse
+import unittest
+import importlib
+
+from typing import Optional
+from unittest.mock import patch
+from utils.utils import download_test_data_using_files_list
+
+
+# list with the test files must be located in the test directory in the repo
+TEST_FILES_LIST = '../test_files_list_in_bucket.txt'
+
+# variables for test config rendering
+INTEGRATION_TESTS_DIR = '{INTEGRATION_TESTS_DIR}'
+TEST_DATA_DIR = '{TEST_DATA_DIR}'
+RESOURCES_DIR = '{RESOURCES_DIR}'
+TRAINING_SETS_DIR = '{TRAINING_SETS_DIR}'
+VARIANT_QC_RANDOM_FOREST_DIR = '{VARIANT_QC_RANDOM_FOREST_DIR}'
+
+def render_config(path_to_template: str, test_data_dir: Optional[str],
+                  resources_dir: Optional[str], training_sets_dir: Optional[str], variant_qc_random_forest_dir: Optional[str],
+                  savefile: str='inputs_test_rendered.yaml'):
+    """
+    Read the config template and fill in the paths.
+    """
+    integration_tests_dir = os.path.dirname(os.path.abspath(__file__))
+
+    # TODO agree on test and resources folder naming convention
+    test_data_dir = test_data_dir if test_data_dir else os.path.join(integration_tests_dir, 'control_set') 
+    resources_dir = resources_dir if resources_dir else os.path.join(integration_tests_dir, 'resources')
+    training_sets_dir = training_sets_dir if training_sets_dir else os.path.join(integration_tests_dir, 'training_sets')
+    variant_qc_random_forest_dir = variant_qc_random_forest_dir if variant_qc_random_forest_dir else os.path.join(integration_tests_dir, 'variant_qc_random_forest_dir')
+
+    with open(path_to_template, 'r') as f:
+        template = f.read()
+
+    # TODO: make versatile
+    template = template.replace(INTEGRATION_TESTS_DIR, integration_tests_dir)
+    template = template.replace(TEST_DATA_DIR, test_data_dir)
+    template = template.replace(RESOURCES_DIR, resources_dir)
+    template = template.replace(TRAINING_SETS_DIR, training_sets_dir)
+    template = template.replace(VARIANT_QC_RANDOM_FOREST_DIR, variant_qc_random_forest_dir)
+
+    with open(savefile, 'w') as f:
+        f.write(template)
+
+# keep an eye on test execution order
+# unittest.TestLoader.sortTestMethodsUsing = None
+
+# DEBUG: might be useful https://spark.apache.org/docs/latest/api/python/getting_started/testing_pyspark.html
+# TODO: clean up hail logs
+
+# /path/to/wes_qc must be in PYTHONPATH
+qc_step_1_1 = importlib.import_module("1-import_data.1-import_gatk_vcfs_to_hail")
+
+qc_step_2_1 = importlib.import_module("2-sample_qc.1-hard_filters_sex_annotation")
+qc_step_2_2 = importlib.import_module("2-sample_qc.2-prune_related_samples")
+qc_step_2_3 = importlib.import_module("2-sample_qc.3-population_pca_prediction")
+qc_step_2_4 = importlib.import_module("2-sample_qc.4-find_population_outliers")
+qc_step_2_5 = importlib.import_module("2-sample_qc.5-filter_fail_sample_qc")
+
+qc_step_3_1 = importlib.import_module("3-variant_qc.variant_qc_non_trios.1-generate_truth_sets_non_trios")
+qc_step_3_2 = importlib.import_module("3-variant_qc.variant_qc_non_trios.2-create_rf_ht_non_trios")
+qc_step_3_3 = importlib.import_module("3-variant_qc.3-train_rf")
+qc_step_3_4 = importlib.import_module("3-variant_qc.4-apply_rf")
+qc_step_3_5 = importlib.import_module("3-variant_qc.variant_qc_non_trios.5-annotate_ht_after_rf_no_trios")
+qc_step_3_6 = importlib.import_module("3-variant_qc.variant_qc_non_trios.6-rank_and_bin_no_trios")
+qc_step_3_7 = importlib.import_module("3-variant_qc.variant_qc_non_trios.7-plot_rf_output_no_trios")
+qc_step_3_8 = importlib.import_module("3-variant_qc.8-select_thresholds")
+qc_step_3_9 = importlib.import_module("3-variant_qc.9-filter_mt_after_variant_qc")
+
+qc_step_4_1 = importlib.import_module("4-genotype_qc.1-apply_hard_filters")
+qc_step_4_1a = importlib.import_module("4-genotype_qc.1a-apply_range_of_hard_filters")
+qc_step_4_2 = importlib.import_module("4-genotype_qc.2-counts_per_sample")
+qc_step_4_3 = importlib.import_module("4-genotype_qc.3-export_vcfs")
+qc_step_4_3a = importlib.import_module("4-genotype_qc.3a-export_vcfs_range_of_hard_filters")
+qc_step_4_3b = importlib.import_module("4-genotype_qc.3b-export_vcfs_stingent_filters")
+
+
+class HailTestCase(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        # get test suite path in the repo
+        test_suite_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+
+        # specify paths to the test data and resources
+        test_data_download_path = os.path.join(test_suite_path, 'test_data_individual_files')
+        test_data_path = os.path.join(test_data_download_path, 'control_set_small')
+        resources_path = os.path.join(test_data_download_path, 'resources')
+        training_sets_path = os.path.join(test_data_download_path, 'training_sets')
+        variant_qc_random_forest_path = os.path.join(test_data_download_path, 'variant_qc_random_forest')
+        ref_data_path = os.path.join(test_data_download_path, 'unit_tests', 'reference_output_data')
+
+        print(f'Downloading data from the bucket using files list {os.path.abspath(TEST_FILES_LIST)}')
+        download_test_data_using_files_list(TEST_FILES_LIST, test_data_download_path)
+
+        smoke_test_dir_path = os.path.dirname(os.path.realpath(__file__))
+        rendered_config_savefile = os.path.join(smoke_test_dir_path, 'integration_config_rendered.yaml')
+        
+        # # render test config from the template
+        # render_config('inputs_test_template.yaml', test_data_path, resources_path) # TODO: make configurable
+        render_config('new_config_test_template.yaml', test_data_path, resources_path, training_sets_path, variant_qc_random_forest_path,
+                      savefile=rendered_config_savefile)
+
+        # set up path to test config
+        os.environ['WES_CONFIG'] = rendered_config_savefile
+
+    @classmethod
+    def tearDownClass(cls):
+        # TODO: clean up logs
+        pass
+
+RF_RUN_TEST_HASH = 'testhash' # manually set rf run id 
+class IntegrationTests(HailTestCase):
+    def test_1_1_import_data(self):
+        try:
+            qc_step_1_1.main()
+        except Exception as e:
+            self.fail(f'Step 1.1 failed with an exception: {e}')
+
+    def test_2_1_sample_qc(self):
+        try:
+            qc_step_2_1.main()
+        except Exception as e:
+            self.fail(f'Step 2.1 failed with an exception: {e}')
+
+    def test_2_2_sample_qc(self):
+        try:
+            qc_step_2_2.main()
+        except Exception as e:
+            self.fail(f'Step 2.2 failed with an exception: {e}')
+
+    # mock cli arguments
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(kg_to_mt=True, run=True, merge=True, filter=True, pca=True, assign_pops=True))
+    def test_2_3_sample_qc(self, mock_args):
+        try:
+            qc_step_2_3.main()
+        except Exception as e:
+            self.fail(f'Step 2.3 failed with an exception: {e}')
+
+    def test_2_4_sample_qc(self):
+        try:
+            qc_step_2_4.main()
+        except Exception as e:
+            self.fail(f'Step 2.4 failed with an exception: {e}')
+
+    def test_2_5_sample_qc(self):
+        try:
+            qc_step_2_5.main()
+        except Exception as e:
+            self.fail(f'Step 2.5 failed with an exception: {e}')
+    
+    # mock cli arguments
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(all=True, truth=True, annotation=True))
+    def test_3_1_variant_qc(self, mock_args):
+        try:
+            qc_step_3_1.main()
+        except Exception as e:
+            self.fail(f'Step 3.1 failed with an exception: {e}')
+    
+    def test_3_2_variant_qc(self):
+        try:
+            qc_step_3_2.main()
+        except Exception as e:
+            self.fail(f'Step 3.2 failed with an exception: {e}')
+
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(manual_runhash=RF_RUN_TEST_HASH))
+    def test_3_3_variant_qc(self, mock_args):
+        try:
+            qc_step_3_3.main()
+        except Exception as e:
+            self.fail(f'Step 3.3 failed with an exception: {e}')
+
+    # mock cli arguments
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(runhash=RF_RUN_TEST_HASH))
+    def test_3_4_variant_qc(self, mock_args):
+        try:
+            qc_step_3_4.main()
+        except Exception as e:
+            self.fail(f'Step 3.4 failed with an exception: {e}')
+
+    # mock cli arguments
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(runhash=RF_RUN_TEST_HASH)) 
+    def test_3_5_variant_qc(self, mock_args):
+        try:
+            qc_step_3_5.main()
+        except Exception as e:
+            self.fail(f'Step 3.5 failed with an exception: {e}')
+
+    # mock cli arguments
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(runhash=RF_RUN_TEST_HASH)) 
+    def test_3_6_variant_qc(self, mock_args):
+        try:
+            qc_step_3_6.main()
+        except Exception as e:
+            self.fail(f'Step 3.6 failed with an exception: {e}')
+
+    # mock cli arguments
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(runhash=RF_RUN_TEST_HASH)) 
+    def test_3_7_variant_qc(self, mock_args):
+        try:
+            qc_step_3_7.main()
+        except Exception as e:
+            self.fail(f'Step 3.7 failed with an exception: {e}')
+
+    # mock cli arguments
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(runhash=RF_RUN_TEST_HASH, snv=92, indel=68))
+    def test_3_8_variant_qc(self, mock_args):
+        try:
+            qc_step_3_8.main()
+        except Exception as e:
+            self.fail(f'Step 3.8 failed with an exception: {e}')
+
+    # mock cli arguments
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(runhash=RF_RUN_TEST_HASH, snv=84, indel=60)) 
+    def test_3_9_variant_qc(self, mock_args):
+        try:
+            qc_step_3_9.main()
+        except Exception as e:
+            self.fail(f'Step 3.9 failed with an exception: {e}')
+
+    # mock cli arguments
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(dp=5, gq=10, ab=0.2)) 
+    def test_4_1_genotype_qc(self, mock_args):
+        try:
+            qc_step_4_1.main()
+        except Exception as e:
+            self.fail(f'Step 4.1 failed with an exception: {e}')
+
+    # mock cli arguments
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(runhash=RF_RUN_TEST_HASH)) 
+    def test_4_1a_genotype_qc(self, mock_args):
+        try:
+            qc_step_4_1a.main()
+        except Exception as e:
+            self.fail(f'Step 4.1a failed with an exception: {e}')
+
+    def test_4_2_genotype_qc(self):
+        try:
+            qc_step_4_2.main()
+        except Exception as e:
+            self.fail(f'Step 4.2 failed with an exception: {e}')
+
+    def test_4_3_genotype_qc(self):
+        try:
+            qc_step_4_3.main()
+        except Exception as e:
+            self.fail(f'Step 4.3 failed with an exception: {e}')
+
+    # mock cli arguments
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(runhash=RF_RUN_TEST_HASH)) 
+    def test_4_3a_genotype_qc(self, mock_args):
+        try:
+            qc_step_4_3a.main()
+        except Exception as e:
+            self.fail(f'Step 4.3a failed with an exception: {e}')
+
+    # mock cli arguments
+    @patch('argparse.ArgumentParser.parse_args',
+    return_value=argparse.Namespace(runhash=RF_RUN_TEST_HASH)) 
+    def test_4_3b_genotype_qc(self, mock_args):
+        try:
+            qc_step_4_3b.main()
+        except Exception as e:
+            self.fail(f'Step 4.3b failed with an exception: {e}')
+
+if __name__ == '__main__':
+    unittest.main()
+
diff --git a/tests/test_files_list_in_bucket.txt b/tests/test_files_list_in_bucket.txt
new file mode 100644
index 0000000..105df0d
--- /dev/null
+++ b/tests/test_files_list_in_bucket.txt
@@ -0,0 +1,45410 @@
+./control_set_small/.control_set_small_chr7.vcf.bgz.crc
+./control_set_small/control_set_small_chr17.vcf.bgz
+./control_set_small/.control_set_small_chr19.vcf.bgz.crc
+./control_set_small/control_set_small_chr9.vcf.bgz
+./control_set_small/control_set_small_chr8.vcf.bgz
+./control_set_small/control_set_small_chr18.vcf.bgz
+./control_set_small/control_set_small_chr22.vcf.bgz
+./control_set_small/.control_set_small_chr6.vcf.bgz.crc
+./control_set_small/control_set_small_chr12.vcf.bgz
+./control_set_small/.control_set_small_chr2.vcf.bgz.crc
+./control_set_small/.control_set_small_chr15.vcf.bgz.crc
+./control_set_small/control_set_small_chr1.vcf.bgz
+./control_set_small/.control_set_small_chr10.vcf.bgz.crc
+./control_set_small/control_set_small_chr19.vcf.bgz
+./control_set_small/.control_set_small_chrY.vcf.bgz.crc
+./control_set_small/.control_set_small_chr14.vcf.bgz.crc
+./control_set_small/control_set_small_chr15.vcf.bgz
+./control_set_small/.control_set_small_chr18.vcf.bgz.crc
+./control_set_small/control_set_small_chr2.vcf.bgz
+./control_set_small/control_set_small_chr10.vcf.bgz
+./control_set_small/.control_set_small_chr13.vcf.bgz.crc
+./control_set_small/.control_set_small_chr3.vcf.bgz.crc
+./control_set_small/control_set_small_chr14.vcf.bgz
+./control_set_small/control_set_small_chrX.vcf.bgz
+./control_set_small/.control_set_small_chr8.vcf.bgz.crc
+./control_set_small/control_set_small_chr3.vcf.bgz
+./control_set_small/control_set_small_chr16.vcf.bgz
+./control_set_small/control_set_small_chr5.vcf.bgz
+./control_set_small/control_set_small_chr6.vcf.bgz
+./control_set_small/.control_set_small_chr12.vcf.bgz.crc
+./control_set_small/control_set_small_chr20.vcf.bgz
+./control_set_small/.control_set_small_chr4.vcf.bgz.crc
+./control_set_small/.control_set_small_chr20.vcf.bgz.crc
+./control_set_small/.control_set_small_chr11.vcf.bgz.crc
+./control_set_small/.control_set_small_chr9.vcf.bgz.crc
+./control_set_small/control_set_small_chr7.vcf.bgz
+./control_set_small/.control_set_small_chr22.vcf.bgz.crc
+./control_set_small/.control_set_small_chr1.vcf.bgz.crc
+./control_set_small/.control_set_small_chrX.vcf.bgz.crc
+./control_set_small/control_set_small_chr21.vcf.bgz
+./control_set_small/.control_set_small_chr5.vcf.bgz.crc
+./control_set_small/.control_set_small_chr17.vcf.bgz.crc
+./control_set_small/control_set_small_chr11.vcf.bgz
+./control_set_small/control_set_small_chrY.vcf.bgz
+./control_set_small/control_set_small_chr13.vcf.bgz
+./control_set_small/.control_set_small_chr21.vcf.bgz.crc
+./control_set_small/.control_set_small_chr16.vcf.bgz.crc
+./control_set_small/control_set_small_chr4.vcf.bgz
+./resources/truthset_table.ht/.README.txt.crc
+./resources/truthset_table.ht/rows/.metadata.json.gz.crc
+./resources/truthset_table.ht/rows/parts/.part-17-91b478ff-51f1-42ea-8134-bfc6ac8350b2.crc
+./resources/truthset_table.ht/rows/parts/part-16-7b384682-8e6c-4ad7-b023-59b9c1212948
+./resources/truthset_table.ht/rows/parts/.part-05-24bcc02c-92d0-4f70-9036-42197ce99bd7.crc
+./resources/truthset_table.ht/rows/parts/.part-02-4d3f4e07-54e9-4777-8b48-3cd8724582ff.crc
+./resources/truthset_table.ht/rows/parts/.part-15-b0433b81-c26b-4af1-91d5-bd97a8dcc4d0.crc
+./resources/truthset_table.ht/rows/parts/.part-18-b35f6a35-7342-47dc-b4df-5db2f21c09ac.crc
+./resources/truthset_table.ht/rows/parts/.part-01-2d26ab73-d528-4c97-8216-9abd22defbe8.crc
+./resources/truthset_table.ht/rows/parts/part-00-72f7c907-794b-4e38-aa17-dce39875c620
+./resources/truthset_table.ht/rows/parts/.part-16-7b384682-8e6c-4ad7-b023-59b9c1212948.crc
+./resources/truthset_table.ht/rows/parts/part-05-24bcc02c-92d0-4f70-9036-42197ce99bd7
+./resources/truthset_table.ht/rows/parts/part-08-1c137a2f-4cb3-48a6-a82a-76debee25f62
+./resources/truthset_table.ht/rows/parts/.part-04-e556cc2f-0d0a-4744-a720-ed3b15b4c91b.crc
+./resources/truthset_table.ht/rows/parts/.part-10-fdec707c-d2fa-4391-b1a2-73983e9629f8.crc
+./resources/truthset_table.ht/rows/parts/part-03-10ce28d5-5223-4881-ae54-03dc87598762
+./resources/truthset_table.ht/rows/parts/part-01-2d26ab73-d528-4c97-8216-9abd22defbe8
+./resources/truthset_table.ht/rows/parts/part-04-e556cc2f-0d0a-4744-a720-ed3b15b4c91b
+./resources/truthset_table.ht/rows/parts/.part-07-e0e313bb-4cf6-4ad7-b5d3-9ab80fbcb533.crc
+./resources/truthset_table.ht/rows/parts/part-06-11c01f00-f2a4-4045-b99f-f0a56b6deb7d
+./resources/truthset_table.ht/rows/parts/part-13-31ae8164-0de7-4e57-a248-399754a1b667
+./resources/truthset_table.ht/rows/parts/part-10-fdec707c-d2fa-4391-b1a2-73983e9629f8
+./resources/truthset_table.ht/rows/parts/.part-03-10ce28d5-5223-4881-ae54-03dc87598762.crc
+./resources/truthset_table.ht/rows/parts/part-07-e0e313bb-4cf6-4ad7-b5d3-9ab80fbcb533
+./resources/truthset_table.ht/rows/parts/part-18-b35f6a35-7342-47dc-b4df-5db2f21c09ac
+./resources/truthset_table.ht/rows/parts/.part-09-0694e4d0-93cc-4ec8-b82f-d7815f01d1e5.crc
+./resources/truthset_table.ht/rows/parts/.part-06-11c01f00-f2a4-4045-b99f-f0a56b6deb7d.crc
+./resources/truthset_table.ht/rows/parts/.part-12-3d08534a-241c-4e2f-ae2d-29ab917a16d2.crc
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+./unit_tests/reference_output_data/matrixtables/mt_hard_filters_annotated.mt/index/part-03-8c154b1b-edc1-43fb-ac0f-99952be1069a.idx/index
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+./unit_tests/reference_output_data/matrixtables/mt_hard_filters_annotated.mt/index/part-04-8a972f61-1b63-4001-b679-2ff6a833491c.idx/index
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+./unit_tests/reference_output_data/matrixtables/mt_hard_filters_annotated.mt/README.txt
+./unit_tests/reference_output_data/matrixtables/mt_hard_filters_annotated.mt/_SUCCESS
+./unit_tests/reference_output_data/matrixtables/mt_hard_filters_annotated.mt/metadata.json.gz
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/.README.txt.crc
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/rows/.metadata.json.gz.crc
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+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/rows/parts/part-0-e4e941d5-2958-4d4c-ba32-2ce35f9b92a6
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/rows/metadata.json.gz
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/._SUCCESS.crc
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/.metadata.json.gz.crc
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/globals/.metadata.json.gz.crc
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/globals/parts/.part-0.crc
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/globals/parts/part-0
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/globals/metadata.json.gz
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+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/index/part-0-e4e941d5-2958-4d4c-ba32-2ce35f9b92a6.idx/.metadata.json.gz.crc
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/index/part-0-e4e941d5-2958-4d4c-ba32-2ce35f9b92a6.idx/index
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/index/part-0-e4e941d5-2958-4d4c-ba32-2ce35f9b92a6.idx/metadata.json.gz
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/README.txt
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/_SUCCESS
+./unit_tests/reference_output_data/matrixtables/pca_loadings_after_pruning.ht/metadata.json.gz
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/cols/.README.txt.crc
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/cols/rows/.metadata.json.gz.crc
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/cols/rows/parts/.part-0.crc
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/cols/rows/parts/part-0
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+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/cols/README.txt
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/cols/_SUCCESS
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/cols/metadata.json.gz
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/.README.txt.crc
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+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/rows/README.txt
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/rows/_SUCCESS
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/rows/metadata.json.gz
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/._SUCCESS.crc
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+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/entries/README.txt
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/entries/_SUCCESS
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+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/globals/.README.txt.crc
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/globals/rows/.metadata.json.gz.crc
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/globals/rows/parts/.part-0.crc
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+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/globals/._SUCCESS.crc
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/globals/.metadata.json.gz.crc
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/globals/globals/.metadata.json.gz.crc
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/globals/globals/parts/.part-0.crc
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/globals/globals/parts/part-0
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/globals/globals/metadata.json.gz
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/globals/README.txt
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/globals/_SUCCESS
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+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/index/part-0-16832af9-6479-40e2-9da3-18b267b4e221.idx/index
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+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/README.txt
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/_SUCCESS
+./unit_tests/reference_output_data/matrixtables/merged_with_1kg.mt/metadata.json.gz
+./unit_tests/reference_output_data/annotations/sex_annotation_f_stat_outliers.txt.bgz
+./unit_tests/reference_output_data/annotations/.sex_annotation_f_stat_outliers.txt.bgz.crc
+./unit_tests/reference_output_data/annotations/sex_annotated.sex_check.txt.bgz
+./unit_tests/reference_output_data/annotations/sample_qc_by_pop.tsv.bgz
+./unit_tests/reference_output_data/annotations/.sex_annotated.sex_check.txt.bgz.crc
+./unit_tests/reference_output_data/annotations/.samples_failing_qc.tsv.bgz.crc
+./unit_tests/reference_output_data/annotations/conflicting_sex.txt.bgz
+./unit_tests/reference_output_data/annotations/.sample_qc_by_pop.globals.json.crc
+./unit_tests/reference_output_data/annotations/.sample_qc_by_pop.tsv.bgz.crc
+./unit_tests/reference_output_data/annotations/samples_failing_qc.tsv.bgz
+./unit_tests/reference_output_data/annotations/sample_qc_by_pop.globals.json
+./unit_tests/reference_output_data/annotations/.conflicting_sex.txt.bgz.crc
diff --git a/tests/unit_tests/test_all_modules.py b/tests/unit_tests/test_all_modules.py
new file mode 100644
index 0000000..ad0f0a0
--- /dev/null
+++ b/tests/unit_tests/test_all_modules.py
@@ -0,0 +1,986 @@
+import os
+import re
+import gzip
+import unittest
+import importlib
+
+import hail as hl
+import shutil as sh
+import hailtop.fs as hfs
+
+from typing import Union
+from pyspark import SparkContext
+from utils.utils import download_test_data_using_files_list
+from utils.config import path_local, path_spark, _process_cvars_in_config
+
+
+def compare_structs(struct1, struct2):
+    """
+    Compare each field in two struct entries.
+    
+    Returns:
+    bool: True if entries are equal, False otherwise.
+    """
+    fields = list(struct1.dtype.fields)
+
+    # if not fields other than key
+    if len(fields) == 0:
+        return hl.bool(True)
+    
+    # Check for NA fields
+    def check_field_equal(field):
+        # expr that field is NA in both entries (MT) or rows (HT)
+        field_not_defined = (~hl.is_defined(struct1[field]) & ~hl.is_defined(struct2[field]))
+        # expr that field is not NA in both entries (MT) or rows (HT)
+        field_defined = hl.is_defined(struct1[field]) & hl.is_defined(struct2[field])
+        # different checks for differenet field dtypes
+        if struct1[field].dtype == hl.dtype('float'):
+            expr = (field_defined & hl.approx_equal(struct1[field], struct2[field])) | field_not_defined
+        elif struct1[field].dtype == hl.dtype('array<float>'):
+            # element_wise_expr = hl.map(lambda a, b: (hl.is_defined(a) & hl.is_defined(b) & hl.approx_equal(a, b)) | (~hl.is_defined(a) & ~hl.is_defined(b)), struct1[field], struct2[field])
+
+            element_wise_expr = hl.map(lambda a, b: (hl.is_defined(a) &
+                                                     hl.is_defined(b) &
+                                                     hl.approx_equal(a, b)) | 
+                                                     (~hl.is_defined(a) & 
+                                                      ~hl.is_defined(b)), 
+                                       struct1[field], struct2[field])
+            expr = hl.all(element_wise_expr)
+        else:
+            # TODO: test for other dtypes
+            expr = (field_defined & (struct1[field] == struct2[field])) | field_not_defined
+        
+        return expr
+
+    comparisons = [check_field_equal(field) for field in fields]
+    return hl.all(lambda x: x, comparisons)
+
+def compare_entries_to_other_mt(this_entry, row_key, col_key, other_mt):
+    """
+    Compare entries of two MatrixTables.
+    
+    Returns:
+    bool: True if entries are equal, False otherwise.
+    """
+    other_entry = other_mt[row_key, col_key]
+    return ~compare_structs(this_entry, other_entry)
+
+def compare_plinks(bed1_path: str, bim1_path: str, fam1_path: str, 
+                   bed2_path: str, bim2_path: str, fam2_path: str) -> bool:
+    """
+    Compare the contents of two Hail plink files.
+
+    Returns:
+    bool: True if the plinks are equal, False otherwise.
+    """
+    # Load the plinks
+    mt1 = hl.import_plink(bed=path_spark(bed1_path), bim=path_spark(bim1_path), fam=path_spark(fam1_path), reference_genome='GRCh38')
+    mt2 = hl.import_plink(bed=path_spark(bed2_path), bim=path_spark(bim2_path), fam=path_spark(fam2_path), reference_genome='GRCh38')
+
+    # Ensure the schemas are the same
+    if mt1.row.dtype != mt2.row.dtype or mt1.col.dtype != mt2.col.dtype or mt1.entry.dtype != mt2.entry.dtype:
+        print('MatrixTable schemas do not match')
+        return False
+
+    # Align row and column keys
+    mt2 = mt2.key_rows_by(*mt1.row_key)  # Reorder row keys to match mt1
+    mt2 = mt2.key_cols_by(*mt1.col_key)  # Reorder column keys to match mt1
+    
+    filtered_mt = mt1.filter_entries(compare_entries_to_other_mt(mt1.entry, mt1.row_key, mt1.col_key, mt2))
+
+    # Check if there are any differing entries
+    num_differences = filtered_mt.entries().count()
+    if num_differences == 0:
+        print('MatrixTables are equal')
+        return True
+    else:
+        print(f'MatrixTables are not equal: {num_differences} differing entries found')
+        return False
+
+def compare_matrixtables(mt1_path: Union[str, hl.MatrixTable], mt2_path: Union[str, hl.MatrixTable]) -> bool:
+    """
+    Compare the contents of two Hail MatrixTables.
+
+    Parameters:
+    mt1_path (str): Path to the first MatrixTable.
+    mt2_path (str): Path to the second MatrixTable.
+
+    Returns:
+    bool: True if the MatrixTables are equal, False otherwise.
+    """
+    # Load the MatrixTables
+    if isinstance(mt1_path, str):
+        mt1 = hl.read_matrix_table(path_spark(mt1_path))
+    elif isinstance(mt1_path, hl.MatrixTable):
+        mt1 = mt1_path
+    else:
+        raise TypeError(f"Expected 'str' or 'hl.Table', but got {type(mt1_path)}")
+    
+    if isinstance(mt2_path, str):
+        mt2 = hl.read_matrix_table(path_spark(mt2_path))
+    elif isinstance(mt2_path, hl.MatrixTable):
+        mt2 = mt2_path
+    else:
+        raise TypeError(f"Expected 'str' or 'hl.Table', but got {type(mt2_path)}")
+
+    # Ensure the schemas are the same
+    if mt1.row.dtype != mt2.row.dtype or mt1.col.dtype != mt2.col.dtype or mt1.entry.dtype != mt2.entry.dtype:
+        print('MatrixTable schemas do not match')
+        return False
+
+    # Align row and column keys
+    mt2 = mt2.key_rows_by(*mt1.row_key)  # Reorder row keys to match mt1
+    mt2 = mt2.key_cols_by(*mt1.col_key)  # Reorder column keys to match mt1
+    
+    filtered_mt = mt1.filter_entries(compare_entries_to_other_mt(mt1.entry, mt1.row_key, mt1.col_key, mt2))
+
+    # Check if there are any differing entries
+    num_differences = filtered_mt.entries().count()
+    if num_differences == 0:
+        print('MatrixTables are equal')
+        return True
+    else:
+        print(f'MatrixTables are not equal: {num_differences} differing entries found')
+        return False
+
+def compare_entries_to_other_ht(this_row_value, row_key, other_ht):
+    """
+    Compare rows of two Tables.
+    
+    Returns:
+    bool: True if entries are equal, False otherwise.
+    """
+    other_row_value = other_ht[row_key]
+    return ~compare_structs(this_row_value, other_row_value)
+
+def compare_tables(ht1_path: Union[str, hl.Table], ht2_path: Union[str, hl.Table]) -> bool:
+    """
+    Compare the contents of two Hail Tables.
+
+    Parameters:
+    ht1_path (str): Path to the first Table.
+    ht2_path (str): Path to the second Table.
+
+    Returns:
+    bool: True if the Tables are equal, False otherwise.
+    """
+    # Load the Tables
+    if isinstance(ht1_path, str):
+        ht1 = hl.read_table(path_spark(ht1_path))
+    elif isinstance(ht1_path, hl.Table):
+        ht1 = ht1_path
+    else:
+        raise TypeError(f"Expected 'str' or 'hl.Table', but got {type(ht1_path)}")
+    
+    if isinstance(ht2_path, str):
+        ht2 = hl.read_table(path_spark(ht2_path))
+    elif isinstance(ht2_path, hl.Table):
+        ht2 = ht2_path
+    else:
+        raise TypeError(f"Expected 'str' or 'hl.Table', but got {type(ht2_path)}")
+
+    # Ensure the schemas are the same
+    if ht1.row.dtype != ht2.row.dtype:
+        print("Table schemas do not match")
+        return False
+
+    # Align row keys
+    ht2 = ht2.key_by(*ht1.key)  # Reorder row keys to match ht1
+
+    rows_differ = ht1.filter(compare_entries_to_other_ht(ht1.row_value, ht1.key, ht2))
+
+    # Check if there are any differing rows
+    num_differences = rows_differ.count()
+
+    if num_differences == 0:
+        print(f'Tables {ht1_path}\n{ht2_path}\nare equal')
+        return True
+    else:
+        print(f'Tables {ht1_path}\n{ht2_path}\nare not equal: {num_differences} differing rows found')
+        return False
+
+def compare_txts(path_1: str, path_2: str, replace_strings: list[list[str, str]] = None) -> bool:
+    """
+    Compare contents of two files based on their raw string content.
+
+    Returns:
+    bool: True if files' contents are equal, False otherwise.
+    """
+    with open(path_1, 'r') as f_1:
+        contents_1 = f_1.read()
+
+    with open(path_2, 'r') as f_2:
+        contents_2 = f_2.read()
+
+    if replace_strings:
+        for pattern, substitute in replace_strings:
+            contents_1 = re.sub(pattern, substitute, contents_1)
+            contents_2 = re.sub(pattern, substitute, contents_2)
+
+    if contents_1 == contents_2:
+        print(f'Files {path_1}\n{path_2}\n are equal')
+    else:
+        print(f'Files {path_1}\n{path_2}\n are not equal')
+
+    return contents_1 == contents_2
+
+def compare_bgzed_txts(path_1: str, path_2: str, replace_strings: list[list[str, str]] = None) -> bool:
+    """
+    Compare contents of two bgzed txt files. 
+    
+    Parameters:
+    replace_strings: list[list[str, str]] - regex and str to replace
+
+    Returns:
+    bool: True if files' contents are equal, False otherwise.
+    """
+    with gzip.open(path_1, 'r') as f_1:
+        contents_1 = f_1.read()
+
+    with gzip.open(path_2, 'r') as f_2:
+        contents_2 = f_2.read()
+    
+    if replace_strings:
+        for pattern, substitute in replace_strings:
+            contents_1 = re.sub(pattern, substitute, contents_1)
+            contents_2 = re.sub(pattern, substitute, contents_2)
+
+    if contents_1 == contents_2:
+        print(f'Files {path_1}\n{path_2}\n are equal')
+    else:
+        print(f'Files {path_1}\n{path_2}\n are not equal')
+
+    return contents_1 == contents_2
+
+# DEBUG: might be useful https://spark.apache.org/docs/latest/api/python/getting_started/testing_pyspark.html
+# TODO: clean up hail logs
+
+# /path/to/wes-qc must be in PYTHONPATH
+qc_step_1_1 = importlib.import_module("1-import_data.1-import_gatk_vcfs_to_hail")
+
+qc_step_2_1 = importlib.import_module("2-sample_qc.1-hard_filters_sex_annotation")
+qc_step_2_2 = importlib.import_module("2-sample_qc.2-prune_related_samples")
+qc_step_2_3 = importlib.import_module("2-sample_qc.3-population_pca_prediction")
+qc_step_2_4 = importlib.import_module("2-sample_qc.4-find_population_outliers")
+qc_step_2_5 = importlib.import_module("2-sample_qc.5-filter_fail_sample_qc")
+
+qc_step_3_1 = importlib.import_module("3-variant_qc.variant_qc_non_trios.1-generate_truth_sets_non_trios")
+qc_step_3_2 = importlib.import_module("3-variant_qc.variant_qc_non_trios.2-create_rf_ht_non_trios")
+qc_step_3_3 = importlib.import_module("3-variant_qc.3-train_rf")
+qc_step_3_4 = importlib.import_module("3-variant_qc.4-apply_rf")
+qc_step_3_5 = importlib.import_module("3-variant_qc.variant_qc_non_trios.5-annotate_ht_after_rf_no_trios")
+qc_step_3_6 = importlib.import_module("3-variant_qc.variant_qc_non_trios.6-rank_and_bin_no_trios")
+qc_step_3_7 = importlib.import_module("3-variant_qc.variant_qc_non_trios.7-plot_rf_output_no_trios")
+qc_step_3_8 = importlib.import_module("3-variant_qc.8-select_thresholds")
+qc_step_3_9 = importlib.import_module("3-variant_qc.9-filter_mt_after_variant_qc")
+
+qc_step_4_1 = importlib.import_module("4-genotype_qc.1-apply_hard_filters")
+qc_step_4_1a = importlib.import_module("4-genotype_qc.1a-apply_range_of_hard_filters")
+qc_step_4_2 = importlib.import_module("4-genotype_qc.2-counts_per_sample")
+qc_step_4_3 = importlib.import_module("4-genotype_qc.3-export_vcfs")
+qc_step_4_3a = importlib.import_module("4-genotype_qc.3a-export_vcfs_range_of_hard_filters")
+qc_step_4_3b = importlib.import_module("4-genotype_qc.3b-export_vcfs_stingent_filters")
+
+
+class HailTestCase(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        # outdir for the outputs of the regression tests
+        cls.test_outdir_path = os.path.dirname(os.path.realpath(__file__))
+
+        # tmp dir for Hail
+        cls.tmp_dir = path_spark(os.path.join(cls.test_outdir_path, 'tmp_test'))
+
+        sc = SparkContext.getOrCreate()
+
+        # initialise Hail in local mode to run the test even without cluster
+        hl.init(sc=sc, app_name="HailTest", master="local[*]",
+                default_reference="GRCh38", tmp_dir=cls.tmp_dir)
+
+    @classmethod
+    def tearDownClass(cls):
+        # clean up tmp_dir
+        hfs.rmtree(cls.tmp_dir)
+        hl.stop()
+
+
+# list with the test files must be located in the test directory in the repo
+TEST_FILES_LIST = '../test_files_list_in_bucket.txt'
+
+class TestQCSteps(HailTestCase):
+    @classmethod
+    def setUpClass(cls):
+        # set up Hail from the base class
+        super(TestQCSteps, cls).setUpClass()
+
+        # `tests/` folder in the repo
+        cls.test_suite_path = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
+
+        cls.test_data_download_path = os.path.join(cls.test_suite_path, 'test_data_individual_files')
+
+        cls.test_data_path = os.path.join(cls.test_data_download_path, 'control_set_small')
+        cls.test_resourcedir = os.path.join(cls.test_data_download_path, 'resources')
+        cls.onekg_resdir = os.path.join(cls.test_resourcedir, 'mini_1000G')
+        cls.training_sets = os.path.join(cls.test_data_download_path, 'training_sets')
+        variant_qc_random_forest_path = os.path.join(cls.test_data_download_path, 'variant_qc_random_forest')
+
+        # download test data from the bucket
+        print(f'Downloading control set from the s3 bucket')
+        download_test_data_using_files_list(TEST_FILES_LIST, cls.test_data_download_path)
+
+
+        # define parameters needed for functions to be tested
+
+        # TODO: separate input resources and annotations from output
+        cls.ref_dataset_path = os.path.join(cls.test_data_download_path, 'unit_tests', 'reference_output_data')
+        cls.ref_mtdir = os.path.join(cls.ref_dataset_path, 'matrixtables')
+        cls.ref_resourcedir = os.path.join(cls.ref_dataset_path, 'resources')
+        cls.ref_annotdir = os.path.join(cls.ref_dataset_path, 'annotations')       
+
+
+        # ===== QC General Params ===== #
+        # output dirs for the regression tests outputs
+        cls.mtdir = os.path.join(cls.test_outdir_path, 'matrixtables_test')
+        cls.annotdir = os.path.join(cls.test_outdir_path, 'annotations_test')
+        cls.plots_dir = os.path.join(cls.test_outdir_path, 'plots_test')
+        cls.var_qc_rf_dir = os.path.join(cls.test_suite_path, 'var_qc_rf_dir_test')
+
+        # add general params into the config object
+        config = dict()
+        config['cvars'] = {
+            'tmpdir': 'general.tmp_dir',
+            'anndir': 'general.annotation_dir',
+            'mtdir': 'general.matrixtables_dir',
+            'resdir': 'general.resource_dir',
+            '1kg_resdir': 'general.onekg_resource_dir',
+            'pltdir': 'general.plots_dir',
+            'traindir': 'general.training_sets_dir',
+            'rfdir': 'general.var_qc_rf_dir'
+        }
+
+        config['general'] = dict(
+            tmp_dir = cls.tmp_dir,
+            annotation_dir = cls.annotdir,
+            matrixtables_dir = cls.mtdir,
+            resource_dir = cls.test_resourcedir,
+            plots_dir = cls.plots_dir,
+            onekg_resource_dir = cls.onekg_resdir, 
+            training_sets_dir = cls.training_sets, 
+            var_qc_rf_dir = cls.var_qc_rf_dir
+        )
+
+        # ===== QC Step 1.1 ===== #
+        # inputs: `cls.test_data_path`
+        cls.vcf_header = '' # not available for the test dataset
+        # outputs
+        cls.output_mt_path = os.path.join(cls.mtdir, 'gatk_unprocessed.mt')
+        # reference outputs
+        cls.ref_mt_file = os.path.join(cls.ref_mtdir, 'gatk_unprocessed.mt')
+
+        # add step 1 parameters into the config obj
+        config['step1'] = dict(
+            gatk_vcf_header_infile = cls.vcf_header,
+            gatk_vcf_indir = cls.test_data_path,
+            gatk_mt_outfile = '{mtdir}/gatk_unprocessed.mt',
+        )
+
+        # ===== QC Step 2.1 ===== #
+        # apply_hard_filters_outputs()
+        # reference inputs
+        cls.ref_unfiltered_mt_path = os.path.join(cls.ref_mtdir, 'gatk_unprocessed.mt')
+        # outputs
+        cls.output_filtered_mt_path = os.path.join(cls.mtdir, 'mt_hard_filters_annotated.mt')
+        # reference outputs
+        cls.ref_output_filtered_mt_path = os.path.join(cls.ref_mtdir, 'mt_hard_filters_annotated.mt')
+
+        # impute_sex()
+        # reference inputs: `cls.ref_output_filtered_mt_path`
+        # outputs
+        cls.output_sex_annotated_path = os.path.join(cls.annotdir, 'sex_annotated.sex_check.txt.bgz')
+        cls.output_sex_mt_path = os.path.join(cls.mtdir, 'mt_sex_annotated.mt')
+        # reference outputs
+        cls.ref_output_sex_annotated_path = os.path.join(cls.ref_annotdir, 'sex_annotated.sex_check.txt.bgz')
+        cls.ref_output_sex_mt_path = os.path.join(cls.ref_mtdir, 'mt_sex_annotated.mt')
+
+        # identify_inconsistencies()
+        # reference inputs: `cls.ref_output_sex_mt_path`
+        # outputs
+        cls.conflicting_sex_path = os.path.join(cls.annotdir, 'conflicting_sex.txt.bgz')
+        cls.sex_annotation_f_stat_outliers_path = os.path.join(cls.annotdir, 'sex_annotation_f_stat_outliers.txt.bgz')
+        # reference outputs
+        cls.ref_conflicting_sex_path = os.path.join(cls.ref_annotdir, 'conflicting_sex.txt.bgz')
+        cls.ref_sex_annotation_f_stat_outliers_path = os.path.join(cls.ref_annotdir, 'sex_annotation_f_stat_outliers.txt.bgz')
+
+        # add step 2.1 parameters into the config obj
+        config['step2'] = dict()
+        config['step2']['sex_annotation_hard_filters'] = dict(
+            filtered_mt_outfile = '{mtdir}/mt_hard_filters_annotated.mt',
+            n_alt_alleles_threshold = 0.001,
+            defined_gt_frac_threshold = 0.99
+        )
+        config['step2']['impute_sex'] = {
+            'sex_ht_outfile': '{anndir}/sex_annotated.sex_check.txt.bgz',
+            'sex_mt_outfile': '{mtdir}/mt_sex_annotated.mt',
+            'female_threshold': 0.5,
+            'male_threshold': 0.8,
+            'aaf_threshold': 0.05
+        }
+        config['step2']['sex_inconsistencies'] = {
+            'sex_metadata_file': '{resdir}/mlwh_sample_and_sex.txt',
+            'conflicting_sex_report_file': '{anndir}/conflicting_sex.txt.bgz',
+            'fstat_outliers_report_file': '{anndir}/sex_annotation_f_stat_outliers.txt.bgz',
+            'fstat_low': 0.2,
+            'fstat_high': 0.8
+        }
+
+        # ===== QC Step 2.2 ===== #
+        # prune_mt()
+        # reference inputs: `cls.ref_output_sex_mt_path`
+        # outputs
+        cls.mt_ldpruned_path = os.path.join(cls.mtdir, 'mt_ldpruned.mt')
+        # reference outputs
+        cls.ref_mt_ldpruned_path = os.path.join(cls.ref_mtdir, 'mt_ldpruned.mt')
+
+        # run_pc_relate()
+        # reference inputs: `cls.ref_mt_ldpruned_path`
+        # outputs
+        cls.relatedness_ht_path = os.path.join(cls.mtdir, 'mt_relatedness.ht')
+        cls._path_path = os.path.join(cls.mtdir, 'mt_related_samples_to_remove.ht')
+        cls.scores_path = os.path.join(cls.mtdir, 'mt_pruned.pca_scores.ht')
+        # reference outputs
+        cls.ref_relatedness_ht_path = os.path.join(cls.ref_mtdir, 'mt_relatedness.ht')
+        cls.ref_samples_to_remove_path = os.path.join(cls.ref_mtdir, 'mt_related_samples_to_remove.ht')
+        cls.ref_scores_path = os.path.join(cls.ref_mtdir, 'mt_pruned.pca_scores.ht')
+
+        # run_population_pca()
+        # reference inputs: `cls.ref_mt_ldpruned_path`, `cls.ref_samples_to_remove_path`
+        # outputs
+        cls.plotdir = os.path.join(cls.test_outdir_path, 'plots_test')
+        cls.plink_path = os.path.join(cls.mtdir, 'mt_unrelated.plink')
+        cls.mt_pca_scores_path = os.path.join(cls.mtdir, 'mt_pca_scores.ht')
+        cls.mt_pca_loadings_path = os.path.join(cls.mtdir, 'mt_pca_loadings.ht')
+        cls.pca_output_path = os.path.join(cls.plotdir, 'pca.html')
+        cls.pca_mt_path = os.path.join(cls.mtdir, 'mt_pca.mt')
+        # reference outputs
+        cls.ref_plink_path = os.path.join(cls.ref_mtdir, 'mt_unrelated.plink')
+        cls.ref_mt_pca_scores_path = os.path.join(cls.ref_mtdir, 'mt_pca_scores.ht')
+        cls.ref_mt_pca_loadings_path = os.path.join(cls.ref_mtdir, 'mt_pca_loadings.ht')
+        cls.ref_pca_output_path = path_local(os.path.join(cls.ref_dataset_path, 'plots', 'pca.html')) # DEBUG: not used
+        cls.ref_pca_mt_path = os.path.join(cls.ref_mtdir, 'mt_pca.mt')
+
+        config['step2']['prune'] = {
+            'pruned_mt_file': '{mtdir}/mt_ldpruned.mt',
+            'ld_prune_args': {'r2': 0.2}
+        }
+
+        config['step2']['prune_pc_relate'] = {
+            'relatedness_ht_file' : '{mtdir}/mt_relatedness.ht',
+            'samples_to_remove_file' : '{mtdir}/mt_related_samples_to_remove.ht',
+            'scores_file': '{mtdir}/mt_pruned.pca_scores.ht',
+            'pca_components': 3,
+            'pc_relate_args': {'min_individual_maf': 0.05,
+                               'block_size' : 4096,
+                               'min_kinship': 0.05,
+                               'statistics': 'kin2',
+                               # k:,
+                               # include_self_kinship:
+                               },         
+            'relatedness_column' : 'kin',
+            'relatedness_threshold': 0.125
+        }
+
+        config['step2']['prune_plot_pca'] = {
+            'plink_outfile' : '{mtdir}/mt_unrelated.plink',
+            'pca_components' : 4,
+            'pca_scores_file' : '{mtdir}/mt_pca_scores.ht',
+            'pca_loadings_file' : '{mtdir}/mt_pca_loadings.ht',
+            'pca_mt_file' : '{mtdir}/mt_pca.mt',
+            'plot_outfile' : '{pltdir}/pca.html'
+        }
+
+        # ===== QC Step 2.3 ===== #
+        # create_1kg_mt()
+        # reference inputs: no
+        # outputs
+        cls.kg_wes_regions = os.path.join(cls.mtdir, 'kg_wes_regions.mt')
+        # reference outputs
+        cls.ref_kg_wes_regions = os.path.join(cls.ref_mtdir, 'kg_wes_regions.mt')
+
+        # merge_with_1kg()
+        # reference inputs: `cls.ref_mt_ldpruned_path`
+        # outputs
+        cls.merged_mt_path = os.path.join(cls.mtdir, 'merged_with_1kg.mt')
+        # reference outputs
+        cls.ref_merged_mt_path = os.path.join(cls.ref_mtdir, "merged_with_1kg.mt")
+
+        # annotate_and_filter()
+        # reference inputs: `cls.ref_merged_mt_path`, `cls.test_resourcedir`
+        # outputs
+        cls.filtered_mt_path = os.path.join(cls.mtdir, 'merged_with_1kg_filtered.mt')
+        # reference outputs
+        cls.ref_filtered_mt_path = os.path.join(cls.ref_mtdir, "merged_with_1kg_filtered.mt")
+
+        # run_pca()
+        # reference inputs: `cls.ref_filtered_mt_path`
+        # outputs
+        cls.pca_scores_path = os.path.join(cls.mtdir, 'pca_scores_after_pruning.ht')
+        cls.pca_loadings_path = os.path.join(cls.mtdir, 'pca_loadings_after_pruning.ht')
+        cls.pca_evals_path = path_local(os.path.join(cls.mtdir, 'pca_evals_after_pruning.txt'))
+        # reference outputs
+        cls.ref_pca_scores_path = os.path.join(cls.ref_mtdir, 'pca_scores_after_pruning.ht')
+        cls.ref_pca_loadings_path = os.path.join(cls.ref_mtdir, 'pca_loadings_after_pruning.ht')
+        cls.ref_pca_evals_path = path_local(os.path.join(cls.ref_mtdir, 'pca_evals_after_pruning.txt'))
+
+        # predict_pops()
+        # reference inputs: `cls.ref_pca_scores_path`
+        # outputs
+        cls.pop_ht_file = os.path.join(cls.mtdir, 'pop_assignments.ht')
+        cls.pop_ht_tsv = os.path.join(cls.mtdir, 'pop_assignments.tsv')
+        # reference outputs
+        cls.ref_pop_ht_file = os.path.join(cls.ref_mtdir, 'pop_assignments.ht')
+        cls.ref_pop_ht_tsv = os.path.join(cls.ref_mtdir, 'pop_assignments.tsv')
+
+        config['step2']['create_1kg_mt'] = {
+            'indir': '{1kg_resdir}',
+            'vcfheader': '{1kg_resdir}/header_20201028.txt',
+            'mt_out_file' : '{mtdir}/kg_wes_regions.mt'
+        }
+
+        config['step2']['merge_with_1_kg'] = {
+            'kg_mt_file' : cls.ref_kg_wes_regions,
+            'merged_mt_outfile' : '{mtdir}/merged_with_1kg.mt'
+        }
+
+        config['step2']['annotate_and_filter'] = {
+            'pops_file' : '{resdir}/igsr_samples.tsv',
+            'call_rate' : 0.99,
+            'AF' : 0.05,
+            'p_value_hwe' : 0.00005,
+            'long_range_ld_file' : '{resdir}/long_ld_regions.hg38.bed',
+            'filtered_mt_outfile' : '{mtdir}/merged_with_1kg_filtered.mt'
+        }
+
+        config['step2']['run_pca'] = {
+            'pca_scores_outfile' : '{mtdir}/pca_scores_after_pruning.ht',
+            'pca_loadings_outfile' : '{mtdir}/pca_loadings_after_pruning.ht',
+            'pca_evals_outfile' : '{mtdir}/pca_evals_after_pruning.txt'
+        }
+        
+        config['step2']['predict_pops'] = {
+            'pca_scores_file' : cls.ref_pca_scores_path,
+            'gnomad_pc_n_estimators' : 100,
+            'gnomad_prop_train' : 0.8,
+            'gnomad_min_prob' : 0.5,
+            'pop_ht_outfile' : '{mtdir}/pop_assignments.ht',
+            'pop_ht_outtsv' : '{mtdir}/pop_assignments.tsv'}
+
+        # ===== QC Step 2.4 ===== #
+        # annotate_mt()
+        # reference inputs: `cls.ref_pop_ht_file`, `cls.ref_pop_ht_tsv`, `cls.ref_mt_file`
+        # outputs
+        cls.annotated_mt_file = os.path.join(cls.mtdir, 'gatk_unprocessed_with_pop.mt')
+        # reference outputs
+        cls.ref_annotated_mt_file = os.path.join(cls.ref_mtdir, 'gatk_unprocessed_with_pop.mt')
+
+        # stratified_sample_qc()
+        # reference inputs: `cls.ref_annotated_mt_file`, `cls.ref_annotdir`
+        # outputs
+        cls.mt_qc_outfile = os.path.join(cls.mtdir, 'mt_pops_sampleqc.mt')
+        cls.ht_qc_cols_outfile = os.path.join(cls.mtdir, 'mt_pops_sampleqc.ht')
+        cls.qc_filter_file = os.path.join(cls.mtdir, 'mt_pops_QC_filters.ht')
+        cls.output_text_file = os.path.join(cls.annotdir, 'sample_qc_by_pop.tsv.bgz')
+        cls.output_globals_json = os.path.join(cls.annotdir, 'sample_qc_by_pop.globals.json')
+
+        # reference outputs
+        cls.ref_mt_qc_outfile = os.path.join(cls.ref_mtdir, 'mt_pops_sampleqc.mt')
+        cls.ref_ht_qc_cols_outfile = os.path.join(cls.ref_mtdir, 'mt_pops_sampleqc.ht')
+        cls.ref_qc_filter_file = os.path.join(cls.ref_mtdir, 'mt_pops_QC_filters.ht')
+        cls.ref_output_text_file = os.path.join(cls.ref_annotdir, 'sample_qc_by_pop.tsv.bgz')
+        cls.ref_output_globals_json = os.path.join(cls.ref_annotdir, 'sample_qc_by_pop.globals.json')
+        
+        config['step2']['annotate_with_pop'] = {
+            'annotated_mt_file' : '{mtdir}/gatk_unprocessed_with_pop.mt'
+        }
+
+        config['step2']['stratified_sample_qc'] = {
+            'mt_qc_outfile': '{mtdir}/mt_pops_sampleqc.mt',
+            'ht_qc_cols_outfile' : '{mtdir}/mt_pops_sampleqc.ht',
+            'qc_filter_file' : '{mtdir}/mt_pops_QC_filters.ht',
+            'min_depth' : 20,
+            'min_genotype_quality' : 20,
+            'min_vaf' : 0.25,
+            'output_text_file' : '{anndir}/sample_qc_by_pop.tsv.bgz',
+            'output_globals_json_file' : '{anndir}/sample_qc_by_pop.globals.json'
+        }
+
+        # ===== QC Step 2.5 ===== #
+        # remove_sample_qc_fails()
+        # reference inputs: `cls.ref_annotated_mt_file`, cls.ref_qc_filter_file`
+        # outputs
+        cls.sample_qc_filtered_mt_file = os.path.join(cls.mtdir, 'mt_pops_QC_filters_after_sample_qc.mt')
+        cls.samples_failing_qc_file = os.path.join(cls.annotdir, 'samples_failing_qc.tsv.bgz')
+        # reference outputs
+        cls.ref_sample_qc_filtered_mt_file = os.path.join(cls.ref_mtdir, 'mt_pops_QC_filters_after_sample_qc.mt')
+        cls.ref_samples_failing_qc_file = os.path.join(cls.ref_annotdir, 'samples_failing_qc.tsv.bgz')
+
+        config['step2']['remove_sample_qc_fails'] = {
+            'samples_failing_qc_file' : '{anndir}/samples_failing_qc.tsv.bgz',
+            'sample_qc_filtered_mt_file' : '{mtdir}/mt_pops_QC_filters_after_sample_qc.mt'
+        }
+
+        # ===== QC Step 3.1 non-trios ===== #
+        # get_truth_ht()
+        # reference inputs:
+        # outputs
+        cls.truth_ht_outfile = os.path.join(cls.test_resourcedir, 'truthset_table.ht')
+        # reference outputs
+        cls.ref_truth_ht_outfile = os.path.join(cls.ref_resourcedir, 'truthset_table.ht')
+
+        # split_multi_and_var_qc()
+        # reference inputs: `` # TODO: fill in
+        # outputs
+        # TODO: fill in
+        # reference outputs
+        cls.ref_mt_varqc_splitmulti = os.path.join(cls.ref_mtdir, 'mt_varqc_splitmulti.mt')
+
+        # ===== QC Step 3.9 ===== #
+        # annotate_mt_with_cq_rf_score_and_bin()
+        # reference inputs: `` # TODO: fill in
+        # outputs
+        # TODO: fill in
+        # reference outputs
+        cls.ref_mt_after_var_qc = os.path.join(cls.ref_mtdir, 'mt_after_var_qc.mt')
+
+
+        # ===== QC Step 4.1 ===== #
+        # filter_mt()
+        # reference inputs: `cls.ref_mt_after_var_qc`
+        # outputs
+        cls.mtfile_filtered = os.path.join(cls.mtdir, 'mt_after_var_qc_hard_filter_gt.mt')
+        # reference outputs
+        cls.ref_mtfile_filtered = os.path.join(cls.ref_mtdir, 'mt_after_var_qc_hard_filter_gt.mt')
+
+        # ===== QC Step 4.1a ===== #
+        # remove_samples()
+        # reference inputs: `cls.ref_mt_varqc_splitmulti`
+
+        
+
+        # ===== QC Step 4.1b ===== #
+
+        # ===== QC Step 4.2 ===== #
+
+        # ===== QC Step 4.3 ===== #
+
+        # ===== QC Step 4.3a ===== #
+
+        # ===== QC Step 4.3b ===== #
+
+
+        cls.config = _process_cvars_in_config(config)
+        
+    # QC Step 1.1
+    def test_1_1_load_vcfs_to_mt(self):
+        # run function to test
+        qc_step_1_1.load_vcfs_to_mt(self.config)
+        
+        # compare the output to reference
+        output_mt_path = self.config['step1']['gatk_mt_outfile']
+        self.assertEqual(output_mt_path, self.output_mt_path)
+
+        outputs_are_identical = compare_matrixtables(self.ref_mt_file, output_mt_path)
+        self.assertTrue(outputs_are_identical)
+
+    # QC Step 2.1 apply_hard_filters
+    def test_2_1_1_apply_hard_filters(self):
+        # read reference output of the step 1.1
+        ref_mt_unfiltered = hl.read_matrix_table(path_spark(self.ref_unfiltered_mt_path))
+
+        # run function to test
+        mt_filtered = qc_step_2_1.apply_hard_filters(ref_mt_unfiltered, self.config)
+        
+        # compare the output to reference
+        output_filtered_mt_path = self.config['step2']['sex_annotation_hard_filters']['filtered_mt_outfile']
+        self.assertEqual(output_filtered_mt_path, self.output_filtered_mt_path)
+        
+        outputs_are_identical = compare_matrixtables(self.ref_output_filtered_mt_path, output_filtered_mt_path)
+        self.assertTrue(outputs_are_identical)
+
+    # QC Step 2.1 impute sex
+    def test_2_1_2_impute_sex(self):
+        # read reference output of the Step 2.1 apply_hard_filters()
+        ref_mt_filtered = hl.read_matrix_table(path_spark(self.ref_output_filtered_mt_path))
+
+        # run function to test
+        sex_mt = qc_step_2_1.impute_sex(ref_mt_filtered, self.config)
+
+        # compare the outputs to reference
+        output_sex_annotated_path = self.config['step2']['impute_sex']['sex_ht_outfile']
+        output_sex_mt_path = self.config['step2']['impute_sex']['sex_mt_outfile']
+        self.assertEqual(output_sex_annotated_path, self.output_sex_annotated_path)
+        self.assertEqual(output_sex_mt_path, self.output_sex_mt_path)
+
+        self.assertEqual(path_local(output_sex_annotated_path), path_local(output_sex_annotated_path))
+
+        output_mts_are_identical = compare_matrixtables(self.ref_output_sex_mt_path, output_sex_mt_path)
+        output_txts_are_identical = compare_bgzed_txts(path_local(self.ref_output_sex_annotated_path),
+                                                       path_local(output_sex_annotated_path))
+
+        self.assertTrue(output_mts_are_identical and output_txts_are_identical)
+
+    def test_2_1_3_identify_inconsistencies(self):
+        # read reference output of the Step 2.1 impute_sex()
+        ref_output_sex_mt = hl.read_matrix_table(path_spark(self.ref_output_sex_mt_path))
+
+        # run function to test
+        qc_step_2_1.identify_inconsistencies(ref_output_sex_mt, self.config)
+
+        # compare outputs to reference
+        conflicting_sex_path = self.config['step2']['sex_inconsistencies']['conflicting_sex_report_file']
+        sex_annotation_f_stat_outliers_path = self.config['step2']['sex_inconsistencies']['fstat_outliers_report_file']
+
+        self.assertEqual(conflicting_sex_path, self.conflicting_sex_path)
+        self.assertEqual(sex_annotation_f_stat_outliers_path, self.sex_annotation_f_stat_outliers_path)
+
+        conflicting_sex_are_identical = compare_bgzed_txts(path_local(self.ref_conflicting_sex_path),
+                                                           path_local(conflicting_sex_path))
+
+        f_stat_outliers_are_identical = compare_bgzed_txts(path_local(self.ref_sex_annotation_f_stat_outliers_path),
+                                                           path_local(sex_annotation_f_stat_outliers_path))
+
+
+        self.assertTrue(conflicting_sex_are_identical and f_stat_outliers_are_identical)
+
+    def test_2_2_1_prune_mt(self):
+        # read reference output of the Step 2.1 impute_sex()
+        ref_output_sex_mt = hl.read_matrix_table(path_spark(self.ref_output_sex_mt_path))
+
+        # run function to test
+        pruned_mt = qc_step_2_2.prune_mt(ref_output_sex_mt, self.config)
+
+        # compare output to reference
+        output_mts_are_identical = compare_matrixtables(self.ref_mt_ldpruned_path, self.mt_ldpruned_path)
+
+        self.assertTrue(output_mts_are_identical)
+
+    def test_2_2_2_run_pc_relate(self):
+        # read reference outputs of the Step 2.2 prune_mt()
+        ref_mt_ldpruned = hl.read_matrix_table(path_spark(self.ref_mt_ldpruned_path))
+
+        # run function to test
+        qc_step_2_2.run_pc_relate(ref_mt_ldpruned, self.config)
+
+        # compare outputs to reference
+        relatedness_ht_path = self.config['step2']['prune_pc_relate']['relatedness_ht_file']
+        samples_to_remove_path = self.config['step2']['prune_pc_relate']['samples_to_remove_file']
+        scores_path = self.config['step2']['prune_pc_relate']['scores_file']
+        
+        output_relatedness_ht_identical = compare_tables(relatedness_ht_path, self.ref_relatedness_ht_path)
+        output_samples_to_remove_identical = compare_tables(samples_to_remove_path, self.ref_samples_to_remove_path)
+        output_scores_identical = compare_tables(scores_path, self.ref_scores_path)
+
+        self.assertTrue(output_relatedness_ht_identical and output_samples_to_remove_identical and output_scores_identical)
+
+    def test_2_2_3_run_population_pca(self):
+        # read reference outputs of Step 2.3
+        # run function to test
+        ref_mt_ldpruned = hl.read_matrix_table(path_spark(self.ref_mt_ldpruned_path))
+        ref_samples_to_remove = hl.read_table(path_spark(self.ref_samples_to_remove_path))
+        qc_step_2_2.run_population_pca(ref_mt_ldpruned, ref_samples_to_remove, self.config)
+        
+        # compare outputs to reference
+        # pca_plots_identical = compare_txts(self.pca_output_path, self.ref_pca_output_path) # TODO: implement robust html comparison
+        pca_scores_identical = compare_tables(self.mt_pca_scores_path, self.ref_mt_pca_scores_path)
+        pca_loadings_identical = compare_tables(self.mt_pca_loadings_path, self.ref_mt_pca_loadings_path)
+        pca_mt_identical = compare_matrixtables(self.pca_mt_path, self.ref_pca_mt_path)
+        plink_identical = compare_plinks(self.plink_path + '.bed', self.plink_path + '.bim', self.plink_path + '.fam', 
+                self.ref_plink_path + '.bed', self.ref_plink_path + '.bim', self.ref_plink_path + '.fam')
+
+        self.assertTrue(pca_scores_identical and pca_loadings_identical and 
+                        pca_mt_identical and plink_identical)
+
+    def test_2_3_1_create_1kg_mt(self):
+        # run function to test
+        qc_step_2_3.create_1kg_mt(self.config)
+        kg_wes_regions_identical = compare_matrixtables(self.kg_wes_regions, self.ref_kg_wes_regions)
+
+        self.assertTrue(kg_wes_regions_identical)
+
+    def test_2_3_2_merge_with_1kg(self):
+        # use reference outputs of Step 2.2 prune_mt()
+        ref_mt_ldpruned = hl.read_matrix_table(path_spark(self.ref_mt_ldpruned_path))
+        # run function to test
+        qc_step_2_3.merge_with_1kg(ref_mt_ldpruned, self.config)
+        merged_mt_identical = compare_matrixtables(self.merged_mt_path, self.ref_merged_mt_path)
+
+        self.assertTrue(merged_mt_identical)
+
+    def test_2_3_3_annotate_and_filter(self):
+        # use reference outputs of Step 2.3 merge_with_1kg()
+        ref_merged_mt = hl.read_matrix_table(path_spark(self.ref_merged_mt_path))
+        # run function to test
+        qc_step_2_3.annotate_and_filter(ref_merged_mt, self.config)
+        filtered_mt_identical = compare_matrixtables(self.filtered_mt_path, self.ref_filtered_mt_path)
+
+        self.assertTrue(filtered_mt_identical)
+
+    def test_2_3_4_run_pca(self):
+        # Use reference output of Step 2.3 annotate_and_filter() as input
+        ref_filtered_mt = hl.read_matrix_table(path_spark(self.ref_filtered_mt_path))
+        # Run function to test
+        qc_step_2_3.run_pca(ref_filtered_mt, self.config)
+
+        # Compare output files to the reference
+        pca_scores_identical = compare_tables(self.pca_scores_path, self.ref_pca_scores_path)
+        pca_loadings_identical = compare_tables(self.pca_loadings_path, self.ref_pca_loadings_path)
+        pca_evals_identical = compare_txts(self.pca_evals_path, self.ref_pca_evals_path)
+
+        # Test passes when all files match the references
+        self.assertTrue(pca_scores_identical and pca_loadings_identical and pca_evals_identical)
+
+    def test_2_3_5_predict_pops(self):
+        # use reference outputs of Step 2.3 run_pca()
+        # run function to test
+        qc_step_2_3.predict_pops(self.config)
+
+        pop_ht_identical = compare_tables(self.pop_ht_file, self.ref_pop_ht_file)
+        pop_ht_tsv_identical = compare_txts(path_local(self.pop_ht_tsv), path_local(self.ref_pop_ht_tsv))
+
+        self.assertTrue(pop_ht_identical and pop_ht_tsv_identical)
+
+    def test_2_4_1_annotate_mt(self):
+        qc_step_2_4.annotate_mt(self.ref_mt_file, self.ref_pop_ht_file, self.annotated_mt_file)
+
+        annotated_mts_identical = compare_matrixtables(self.annotated_mt_file, self.ref_annotated_mt_file)
+
+        self.assertTrue(annotated_mts_identical)
+
+    def test_2_4_2_stratified_sample_qc(self):
+        qc_step_2_4.stratified_sample_qc(self.ref_annotated_mt_file, self.mt_qc_outfile,
+                self.ht_qc_cols_outfile, self.qc_filter_file, self.config)
+
+        mt_qc_identical = compare_matrixtables(self.mt_qc_outfile, self.ref_mt_qc_outfile)
+        ht_qc_cols_identical = compare_tables(self.ht_qc_cols_outfile, self.ref_ht_qc_cols_outfile)
+        qc_filter_identical = compare_tables(self.qc_filter_file, self.ref_qc_filter_file)
+        out_text_identical = compare_bgzed_txts(path_local(self.output_text_file), 
+                path_local(self.ref_output_text_file))
+
+        unique_hail_id_replace = [[r'__uid_\d+\n', '']] # compare files up to a unique Hail file id
+        out_globals_json_identical = compare_txts(path_local(self.output_globals_json), 
+                path_local(self.ref_output_globals_json), replace_strings=unique_hail_id_replace)
+
+        self.assertTrue(mt_qc_identical and ht_qc_cols_identical and 
+                qc_filter_identical and out_text_identical and out_globals_json_identical)
+
+    def test_2_5_1_remove_sample_qc_fails(self):
+        qc_step_2_5.remove_sample_qc_fails(self.ref_annotated_mt_file, self.ref_qc_filter_file,
+                self.samples_failing_qc_file, self.sample_qc_filtered_mt_file)
+
+        sample_qc_filtered_identical = compare_matrixtables(self.sample_qc_filtered_mt_file, 
+                self.ref_sample_qc_filtered_mt_file)
+        samples_failing_qc_identical = compare_bgzed_txts(path_local(self.samples_failing_qc_file),
+                path_local(self.ref_samples_failing_qc_file))
+
+        self.assertTrue(sample_qc_filtered_identical and samples_failing_qc_identical)
+
+
+    # tests for 4-genotype_qc
+    def test_4_1_1_filter_mt(self):
+        qc_step_4_1.filter_mt(self.ref_mt_after_var_qc, dp=5, gq=10, ab=0.2, 
+                              mtfile_filtered=self.mtfile_filtered)
+
+        mtfile_filetered_identical = compare_matrixtables(self.mtfile_filtered, self.ref_mtfile_filtered)
+
+        self.assertTrue(mtfile_filetered_identical)
+
+    # TODO: implement tests for the remaining functions listed below
+
+    # test data has no trios, so only non-trios scripts are tested
+    def test_3_non_trios_1_1_get_truth_ht(self):
+        pass
+
+    def test_3_non_trios_1_2_split_multi_and_var_qc(self):
+        pass
+
+    def test_3_non_trios_1_3_create_inbreeding_ht_with_ac_and_allele_data(self):
+        pass
+
+    def test_3_non_trios_2_1_create_rf_ht(self):
+        pass
+
+    def test_3_non_trios_5_1_add_cq_annotation(self):
+        pass
+
+    def test_3_non_trios_5_2_annotate_gnomad(self):
+        pass
+
+    def test_3_non_trios_6_1_add_rank(self):
+        # NOTE: the output of this function in modified in main, 
+        # so a proper reference must be generated manually
+        pass
+
+    def test_3_non_trios_6_2_create_binned_data_initial(self):
+        pass
+
+    def test_3_3_1_get_rf_runs(self):
+        # NOTE: maybe not needed as it doesn't use hail
+        pass
+
+    def test_3_3_2_train_rf(self):
+        pass
+
+    def test_3_3_3_get_run_data(self):
+        # NOTE: maybe not needed as it doesn't use hail
+        pass
+
+    def test_3_9_1_annotate_mt_with_cq_rf_score_and_bin(self):
+        pass
+
+    def test_4_1a_1_remove_samples(self):
+        # not used during qc (commented out)
+        # TODO: implement when clarified the purpose of the function
+        pass
+
+    def test_4_1a_2_annotate_cq_rf(self):
+        # qc_step_4_1a.annotate_cq_rf(self.ref_mt_varqc_splitmulti, self.ref_all_consequences_with_gene_and_csq)
+        # TODO: save the resulting mt in the main() function of the script to generate reference output
+        pass
+
+    def test_4_1a_3_apply_hard_filters(self):
+        # qc_step_4_1a.apply_hard_filters(...)
+        pass
+
+    def test_4_2_1_annotate_gnomad(self):
+        # TODO: generate reference outputs for this function
+        pass
+
+    def test_4_2_2_get_counts_per_cq(self):
+        pass
+
+    def test_4_2_3_get_ca_fractions(self):
+        pass
+
+    def test_4_3_1_export_vcfs(self):
+        pass
+
+    def test_4_3a_1_export_vcfs(self):
+        pass
+
+    def test_4_3b_1_export_vcfs(self):
+        pass
+
+    @classmethod
+    def tearDownClass(cls):
+        # clean up the directories created by the QC steps
+        if hfs.is_dir(cls.mtdir):
+            hfs.rmtree(cls.mtdir) 
+        if hfs.is_dir(cls.annotdir):
+            hfs.rmtree(cls.annotdir)
+        if os.path.exists(cls.plotdir):
+            sh.rmtree(cls.plotdir)
+        super(TestQCSteps, cls).tearDownClass()
+
+
+if __name__ == '__main__':
+    unittest.main()
+
diff --git a/utils/config.py b/utils/config.py
new file mode 100644
index 0000000..da7eeba
--- /dev/null
+++ b/utils/config.py
@@ -0,0 +1,425 @@
+"""
+A separate file with minimal dependencies
+"""
+
+import os
+import sys
+import yaml
+import re
+from typing import Iterable
+
+"""
+Config utils
+"""
+
+def get_script_path() -> str:
+    #returns the path of the script that is being run
+    return os.path.dirname(os.path.realpath(sys.argv[0]))
+
+# TODO: move this stuff to another utils file. Something like `common.py`
+
+def getp(_dict: dict, keypath: str, silent: bool = False, default = None):
+    """
+    getPath: Get a value from a tree of dicts using dot-notation. That is, 
+    `getp(conf, "a.b.c") == conf['a']['b']['c']`
+
+    - `_dict` is a structure of nested dicts
+    - `keypath` is a sequence of keys joined by '.'
+    - if `silent` then return `default` value on invalid path instead of raising an exception  
+
+    Note that this function can return a dict as well as a scalar -- it has no output type checks.
+    """
+    keyseq = keypath.strip('.').split('.')
+    if keyseq[0] not in _dict:
+        if silent: return default
+        raise KeyError(f"top-level dict has no '{keyseq[0]}' key")
+    
+    section = _dict
+    breadcrumbs = ''
+    for nextkey in keyseq:
+        if isinstance(section, dict):
+            if nextkey in section:
+                section = section[nextkey]
+                breadcrumbs += '.' + nextkey
+            else:
+                if silent: return default
+                raise KeyError(f"{keypath} : '{breadcrumbs}' section has no '{nextkey}' field")
+        else:
+            if silent: return default
+            raise KeyError(f"{keypath} : {breadcrumbs + '.' + nextkey} is a field, not a section")
+    return section
+
+def checkp(_dict: dict, keypath: str):
+    """
+    checkPath: Check if a value is in a nested dict using dot-notation. That is, 
+    `checkp(conf, "a.b.c")` is True if `conf['a']['b']['c']` is valid.
+    That is, `conf['a']` and `conf['a']['b']` are dicts and `conf['a']['b']['c']` is 
+    either a dict or a value.  
+    This function will not check if a value is a dict or a field.
+
+    Parameters
+    - `_dict` is a nested dict
+    - `keypath` is a sequence of keys joined by '.'
+    """
+    keyseq = keypath.strip('.').split('.')
+    if keyseq[0] not in _dict:
+        return False
+    
+    section = _dict
+    breadcrumbs = ''
+    for nextkey in keyseq:
+        if isinstance(section, dict):
+            if nextkey in section:
+                section = section[nextkey]
+                breadcrumbs += '.' + nextkey
+            else:
+                return False
+        else:
+            return True
+    return True
+
+def subdict(_dict: dict, keys: Iterable[str]) -> dict:
+    """
+    Get a subset of a dictionary safely. Output dictionary will only have those keys that are in both _dict and keys list.
+
+    Useful for constructing a kwargs dict
+    """
+    correct_keys = _dict.keys() & set(keys)
+    return {k: _dict[k] for k in correct_keys}
+
+def multigetp(_dict: dict, keypaths: Iterable[str], silent: bool = False, default = None) -> tuple:
+    """
+    MultiGetPath: Get a series of items by keys using `utils.getp`.
+    Useful when you want to get several items at once (via unpacking).
+    """
+    return (getp(_dict, k, silent, default) for k in keypaths)
+
+import collections
+def flatten(dictionary: collections.abc.MutableMapping, parent_key=False, separator='.') -> dict:
+    """
+    Turn a nested dictionary into a flattened dictionary.
+
+    Maintains an insertion order.
+    From https://stackoverflow.com/a/62186053
+
+    :param dictionary: The dictionary to flatten
+    :param parent_key: The string to prepend to dictionary's keys.
+    :param separator: The string used to separate flattened keys
+    :return: A flattened dictionary
+    """
+
+    items = []
+    for key, value in dictionary.items():
+        new_key = str(parent_key) + separator + key if parent_key else key
+        if isinstance(value, collections.abc.MutableMapping):
+            items.extend(flatten(value, new_key, separator).items())
+        else:
+            items.append((new_key, value))
+    return dict(items)
+
+def flat_to_nested(flat_dictionary: collections.abc.MutableMapping, parent_key=None, separator='.') -> dict:
+    """
+    Turn a flat dictionary with `separator`-separated keys into a nested dictionary.
+    Maintains an insertion order only for fields.
+
+    :param dictionary: A flat dictionary to transform to a nested one 
+    :param parent_key: The string to prepend to dictionary's keys
+    :param separator: The string used to separate flattened keys (default ".", a dot)
+    :return: A nested dictionary
+    """
+
+    nested_dict = dict()
+
+    for key, value in flat_dictionary.items():
+        keyp = key.strip(separator).split(separator)
+        section = nested_dict
+        for k in keyp[:-1]:
+            if k not in section:
+                section[k] = dict()
+            section = section[k]
+        section[keyp[-1]] = value
+
+    return nested_dict
+
+def is_subsection(subsection_key: str, supersection_key: str) -> bool:
+    """
+    Compare two string keys for a nested directory in a dot-notation.
+    Return True if `subsection_key` is a possible field of a dict at `supersection_key`.
+
+    Examples: 
+    - `is_subsection('foo.bar.baz', 'foo.bar') == True`
+    - `is_subsection('foo.bar.baz', 'foo') == True`
+    - `is_subsection('any.other.key', '') == True`
+    """
+    if supersection_key == '': 
+        return True
+    return subsection_key.startswith(supersection_key + '.')
+
+def parent_section(section_key: str) -> str:
+    """
+    Extract a parent section for a nested dictionary string key in a dot notation.
+
+    Examples: 
+    - `parent_section('foo.bar.baz') == 'foo.bar'`
+    - `parent_section('foo') == ''`
+    - `parent_section('') == ''`
+    """
+    dot_idx = section_key.rfind('.')
+    if dot_idx < 0: return ''
+    return section_key[:dot_idx]
+
+def resolve_cvar_flat(cvar_expr: str, flat_base_config: dict, fieldname: str = '', undefined_ok: bool = False) -> str:
+    """
+    Get a value that cvar (without braces) should be substituted with.
+    
+    Parameters:
+    - cvar_expr: a cvar expression without braces. A field key in a nested dict, or a cvar constant
+    - flat_base_config: a FLAT config, a context for cvar resolution. cvar_expr will be resolved using data from flat_base_config
+    - fieldname: an optional key of the field that contains this cvar (in a dot-notation).  
+        This is used to resolve local config variables and for logging
+    - undefined_ok: If True and a cvar expression cannot be resolved, then return it as it is.  
+        If False, throw a ValueError in that case.
+
+    - If cvar_expr is a cvar shortcut (a name defined in cvars section), then use the field it refers to
+    - If cvar_expr is a field name then 
+        - try to use a field with that key in the same section (you can skip this by starting your cvar_expr with a dot "{.foo.bar}")
+        - try to find that field in the whole config 
+    - If cannot find a suitable value and undefined_ok is False, raise a ValueError
+    - If cannot find a suitable value and undefined_ok is True, return None 
+    """
+    try:    
+        # 1. cvar shortcuts. Always absolute. At most once.
+        cvar_shortcut_def = f"cvars.{cvar_expr}"
+        if cvar_shortcut_def in flat_base_config:
+            if undefined_ok:
+                return flat_base_config.get(flat_base_config[cvar_shortcut_def], '{'+cvar_expr+'}')
+            return flat_base_config[flat_base_config[cvar_shortcut_def]]
+
+        # 2. config variable in the same section, providing we have a fieldname.
+        #    skip if cvar is explicit full key (starts with `.`).
+        if cvar_expr[0] != '.':
+            cvar_as_local = f"{parent_section(fieldname)}.{cvar_expr}"
+            if fieldname and (cvar_as_local in flat_base_config):
+                return flat_base_config[cvar_as_local]
+            # note that we still need to check a full key
+        
+        # 3. config variable with a full key
+        if cvar_expr[0] == '.':
+            cvar_expr = cvar_expr[1:]
+        if undefined_ok:
+            return flat_base_config.get(cvar_expr, '{'+cvar_expr+'}')
+        return flat_base_config[cvar_expr]
+
+    except KeyError as e:
+        raise ValueError(f"cannot substitute undefined config variable '{cvar_expr}' referenced in field '{fieldname}'")
+
+"""
+Detect field names that end in dir, file, indir, outdir, infile, outfile + optionally _local.
+Capture groups are (in/out/None, dir/file, _local/None).  
+The first group does not matter for a match, but is useful for parsing. 
+"""
+__is_path_field_re = re.compile(r"(out|in)?(dir|file)(_local)?$")
+def __is_path_field(fieldname: str):
+    return __is_path_field_re.search(fieldname) is not None
+
+def _expand_cvars_str(base_config: dict, str_with_cvar: str, fieldname: str, as_path: bool = False, undefined_ok: bool = False):
+    """
+    Substitute config variables in a string.  
+    You can specify config field alisases in `cvars` config section to avoid specifying the full field name for frequently used fields.  
+    If undefined_ok, ignore errors, leave invalid cvars as is.
+
+    :param dict base_config: a flat config dictionary and a source for values to substitute
+    :param str str_with_cvar: a string with a variable that will be substituted by value from `base_config`
+    :param str fieldname: a name of this string field for logging purposes
+    :param bool as_path: shall this string be treated as a file/dir path
+    :param bool undefined_ok: shall we ignore undefined variables, or raise an exception
+    
+    Perform basic path normalization if `as_path`.
+    
+    Will use `cvars` section from the `base_config` first, 
+    and literal field names from the `base_config` second.
+    """
+
+    # Find all cvars that look like {something}
+    # - no dots at the begininng or at the end
+    # - no more 1 dot in a row
+    # - a-zA-Z0-9_ as identifiers
+    cvar_re = re.compile(r"\{([a-zA-Z0-9_]+(?:\.[a-zA-Z0-9_]+)*)\}")
+    def repl(cvar_match):
+        cvar_expr = cvar_match.group(1)
+        return str(resolve_cvar_flat(cvar_expr, base_config, fieldname, undefined_ok))
+    expanded_str = cvar_re.sub(repl, str_with_cvar)
+
+    if as_path:
+        # separate protocol beforehand because os.path.normalize does bad things to URIs
+        proto_re = re.compile(r"[a-zA-Z][a-zA-Z0-9]*:\/\/")
+        proto_match = proto_re.match(expanded_str.strip())
+        if proto_match is not None: 
+            expanded_str = expanded_str[proto_match.end():]
+        # normalize path
+        expanded_str = os.path.normpath(expanded_str) if expanded_str else ''
+        # restore the protocol
+        if proto_match is not None:
+            expanded_str = proto_match[0] + expanded_str
+
+    return expanded_str
+
+def _process_cvars_in_flat_config(flat_unprocessed_config: dict, base_config: dict = dict()):
+    """
+    Recursively expand cvars in all string fields in a FLAT `unprocessed_config`
+    using data from `base_config`.  
+    Detect and activate path mode automatically based on __is_path_field.
+    Specify additional config field aliases in `custom_shortcuts`.
+
+    :param dict flat_unprocessed_config: a flat dictionary with string values that needs cvar expansion
+    :param dict base_config: a read-only dictionary, a base config, that will act as an additional source for config variables
+    :return dict: a FLAT config with all cvar expression replaced (where possible)
+
+    Order of config variable resolution:
+    1. `cvars` section from the unprocessed_config
+    2. `cvars` section from the base_config
+    3. unprocessed_config fields in same section
+    4. base_config fields in same section
+    5. unprocessed_config fields by full key
+    6. base_config fields by full key
+    """
+
+    # the full context for variable substitution
+    context = base_config.copy()
+    # we only need cvar shortcuts for now
+    for k,v in flat_unprocessed_config.items():
+        if k.startswith('cvar_shortcuts.'):
+            context[k] = v
+    # note that context does not contain unprocessed_config at start, but will contain in the end
+    config = flat_unprocessed_config.copy()
+
+    for key in config:
+        val = config[key]
+        if isinstance(val, str):
+            processed_str = _expand_cvars_str(context, val, key, as_path=__is_path_field(key))
+            context[key] = processed_str
+            config[key] = processed_str
+        elif isinstance(val, dict):
+            raise ValueError(f"This function accepts only a flat config. Nested dict detected at {key=}")
+
+    return config
+
+def _process_cvars_in_config(unprocessed_config: dict, base_config: dict = dict()):
+    """
+    Same as utils.config._process_cvars_in_flat_config, but supports both NESTED and FLAT configs.
+
+    If input config is FLAT, output config will be FLAT. If input config is NESTED, output config will be NESTED.
+
+    :param dict unprocessed_config: a flat dictionary with string values that needs cvar expansion
+    :param dict base_config: a read-only dictionary, a base config, that will act as an additional source for config variables
+    :return dict: a FLAT config with all cvar expression replaced (where possible)
+
+    NOTE: _process_cvars_in_flat_config is a backward-compatible way to introduce flat configs, as it is a difficult task to refactor all config usages *again*.
+    """
+    is_flat_config = any(map((lambda key: '.' in key), unprocessed_config.keys()))
+    is_nested_config = any(map((lambda v: isinstance(v, dict)), unprocessed_config.values()))
+
+    if is_flat_config and is_nested_config:
+        raise ValueError("Cannot determine wether unprocessed_config is FLAT or NESTED")
+    if not is_flat_config and not is_nested_config:
+        # Only top-level fields, config is both flat and nested.
+        # Using flat to increase performance a bit.
+        is_flat_config = True
+
+    flat_unprocessed_config = flatten(unprocessed_config) if is_nested_config else unprocessed_config
+    flat_config = _process_cvars_in_flat_config(flat_unprocessed_config)
+    return flat_to_nested(flat_config) if is_nested_config else flat_config
+
+def parse_config_file(file_obj, additional_cvar_shortcuts: dict = dict()):
+    config = yaml.safe_load(file_obj)
+    if 'cvars' not in config:
+        config['cvars'] = dict()
+    config['cvars'].update(additional_cvar_shortcuts)
+    # NOTE mk43: This will use NESTED config style
+    # TODO mk43: Replace with FLAT config style in future
+    #            using `config = flatten(config)`
+    config = _process_cvars_in_config(config)
+    return config
+
+# TODO: rename to load_config or get_config
+def parse_config(path: str = None, additional_cvar_shortcuts: dict = dict()):
+    """
+    Read and parse WES QC YAML config from default location, env variable, or function argument.  
+    Does variable substitution via `_process_cvars_in_config`.
+    
+    Config lookup order:
+    1. `path` if it is not None
+    2. `$WES_CONFIG` if `WES_CONFIG` env variable starts with `/` or `./`
+    3. `../config/$WES_CONFIG` and `../../config/$WES_CONFIG`
+    4. `../config/input.yaml` and `../../config/input.yaml`
+    """
+
+    # with an option to get the config file path from env or from arg
+    
+    if path is not None:
+        print(f"Loading config '{path}', function arg")
+        with open(path, 'r') as y:
+            config = parse_config_file(y, additional_cvar_shortcuts)
+        return config
+    
+    # find config dir
+    script_dir = get_script_path()
+    print("info: script_dir ", script_dir)
+    config_dir = '../config'
+    # to handle 3-variant_qc subdirs 
+    if not os.path.exists(os.path.join(script_dir, config_dir)):
+        config_dir = '../../config'
+    config_dir = os.path.join(script_dir, config_dir)
+    
+    # default values
+    input_yaml = os.path.join(config_dir, 'inputs.yaml')
+    config_type = 'default'
+    
+    # handle environmental variable
+    if 'WES_CONFIG' in os.environ:
+        config_path = os.environ['WES_CONFIG']
+        if config_path[0] == '/' or config_path.startswith('./'):
+            # an absolute path
+            input_yaml = config_path
+            config_type = 'WES_CONFIG absolute'
+        else:
+            # consider path as relative to the config dir!
+            input_yaml = os.path.join(config_dir, config_path)
+            config_type = 'WES_CONFIG relative to config dir'
+
+    # read config
+    if not os.path.exists(input_yaml):
+        print(f"error: config {input_yaml} does not exist")
+    print(f"Loading config '{input_yaml}', {config_type}")
+        
+    with open(input_yaml, 'r') as y:
+        config = parse_config_file(y, additional_cvar_shortcuts)
+
+    return config
+
+
+"""
+Path utils
+"""    
+
+def path_spark(path: str):
+    """
+    Ensure `path` is a valid spark path. 
+    That is, add 'file://' prefix if needed
+    """
+    if path.startswith('file://'):
+        return path
+    if path.startswith('hdfs://'):
+        raise NotImplementedError('Cannot convert hdfs to a spark path')
+    return 'file://' + path
+
+def path_local(path: str):
+    """
+    Ensure `path` is a valid linux path. 
+    That is, remove 'file://' prefix if needed
+    """
+    if path.startswith('file://'):
+        return path[7:]
+    if path.startswith('hdfs://'):
+        raise NotImplementedError('Cannot convert hdfs to a local path')
+    return path
diff --git a/utils/utils.py b/utils/utils.py
index 287aa54..2e4dc68 100644
--- a/utils/utils.py
+++ b/utils/utils.py
@@ -1,27 +1,33 @@
 # useful functions
 import os
 import sys
-import yaml
 import hail as hl
+from gnomad.resources.resource_utils import TableResource
 import pandas as pd
 from shutil import rmtree
 from typing import Optional, Union, Set
-from gnomad.resources.resource_utils import TableResource
-
-def get_script_path():
-    #returns the path of the script that is being run
-    return os.path.dirname(os.path.realpath(sys.argv[0]))
-
-def parse_config():
-    script_dir = get_script_path()
-    input_yaml = script_dir + '/../config/inputs.yaml'
-    if not os.path.exists(input_yaml):
-        input_yaml = script_dir + '/../../config/inputs.yaml'
-    with open(input_yaml, 'r') as y:
-        inputs = yaml.load(y, Loader=yaml.FullLoader)
-
-    return inputs
 
+"""
+Config
+"""
+
+# TODO: cleanup these imports
+from utils.config import (
+    getp,
+    subdict,
+    multigetp,
+    __is_path_field_re,
+    __is_path_field,
+    _expand_cvars_str,
+    _process_cvars_in_flat_config,
+    parse_config,
+    path_local,
+    path_spark
+)
+
+"""
+Other
+"""
 
 def expand_pd_array_col(
         df: pd.DataFrame,
@@ -69,9 +75,9 @@ def get_rf(
     :param str run_hash: Hash of RF run to load
     :return: Path to desired RF data
     """
-    hashdir = rf_dir + run_hash + "/"
-    model_file = hashdir + "rf.model"
-    data_file = hashdir + data + ".ht"
+    hashdir = os.path.join(rf_dir, run_hash)
+    model_file = os.path.join(hashdir, "rf.model")
+    data_file = os.path.join(hashdir, data + ".ht")
     if data == "model":
         return model_file
     else:
@@ -79,7 +85,7 @@ def get_rf(
 
 
 def rm_mt(path: str):
-    rmtree(path.replace('file:/', '/'))
+    rmtree(path_local(path))
 
 
 def collect_pedigree_samples(ped: hl.Pedigree) -> Set[str]:
@@ -93,3 +99,82 @@ def select_founders(ped: hl.Pedigree) -> Set[str]:
     for trio in ped.trios:
         samples.discard(trio.s)
     return samples
+
+import subprocess
+
+# === Utils for downloading test data from the s3 storage === #
+
+TEST_DATA_FILENAME = 'all_test_data.zip'
+TEST_DATA_ARCHIVE_URL = f'https://wes-qc-data.cog.sanger.ac.uk/all_test_data/{TEST_DATA_FILENAME}'
+TEST_DATA_PARENT_DIR_URL = 'https://wes-qc-data.cog.sanger.ac.uk'
+TEST_DATA_DIR_NAMES = ['control_set_small', 'unit_tests', 'resources', 'training_sets']
+
+# TODO: download using a .txt file with the list of all files instead of archiving
+# TODO: test this draft
+def download_test_data_using_files_list(files_list: str, outdir: str) -> None:
+    """ `files_list` must be generated with the following command ran from the directory with the test data:
+    ```
+    find . -print > ../files_list.txt
+    ```
+    Then it can be used as an input to this function.
+    """
+    with open(files_list, 'r') as f:
+        all_files = f.readlines()[1:] # skip the current dir row
+
+    downloaded_test_dirs = [test_dir for test_dir in TEST_DATA_DIR_NAMES if os.path.exists(os.path.join(outdir, test_dir))]    
+    print(f"Test folders {', '.join(downloaded_test_dirs)} already downloaded")
+
+    for file_path in all_files:
+        file_path = file_path.rstrip()
+        file_path_relative_to_current_dir = file_path.replace('./', '', 1)
+        data_folder = file_path_relative_to_current_dir.split('/')[0] # TODO: optimise
+        
+        # naive approach - if parent dir of the file already exists, don't download the file
+        if data_folder in downloaded_test_dirs:
+            continue
+
+        file_url = file_path.replace('.', TEST_DATA_PARENT_DIR_URL, 1) # create download urls for each file
+        file_destination = os.path.dirname(os.path.normpath(os.path.join(outdir, file_path_relative_to_current_dir))) # remove possible double slashes
+
+        subprocess.run(['wget', '-nv', '-nc', file_url, '-P', file_destination]) # downlaod the file into destination
+
+def move_dirs(move_dirs: dict) -> None:
+    print(f'Copying data to correct dirs')
+    for dir_to_move, destination_dir in move_dirs.items():
+        subprocess.run(['cp', '-vnr', dir_to_move, destination_dir])
+
+# TODO: make versatile, don't download if already exists
+def download_test_data_from_s3(outdir: str, move_dirs: dict, clean_up_unzip_dir: bool = False) -> None:
+    """Download compressed test data from the s3 storage and 
+    move the subfolders to the correct destinations inside the repo.
+
+    Parameters
+    ----------
+    outdir : str
+        Path to download and extract compressed test data.
+    
+    move_dirs : dict
+        Directories to move. Keys are the dirs to be moved, values are their destination dirs
+    
+    clean_up_unzip_dir : bool, default: False
+        Remove the folder with the unzipped data after moving the data from it.
+
+    Return
+    ------
+        None
+    """
+    print(f'Downloading data from the s3 bucket') # TODO: improve logging
+    # Download zipped archive with all the data
+    subprocess.run(['wget', '-nc', TEST_DATA_ARCHIVE_URL, '-P', outdir]) # skip existing
+
+    # Unzip the data
+    print(f'Unzipping the data')
+    subprocess.run(['unzip', '-n', os.path.join(outdir, TEST_DATA_FILENAME), '-d', outdir])
+    # Move unzipped data to correct folders in the test dir
+    print(f'Copying data to correct dirs')
+
+    for dir_to_move, destination_dir in move_dirs.items():
+        subprocess.run(['cp', '-vnr', dir_to_move, destination_dir])
+
+    if clean_up_unzip_dir:
+        subprocess.run(['rm', '-r', outdir])