small fix

wtsi-hgi · Apr 2, 2024 · ba93796 · ba93796
1 parent 526ae89
commit ba93796
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Showing 4 changed files with 12 additions and 5 deletions.
diff --git a/conf/base.conf b/conf/base.conf
@@ -27,7 +27,7 @@ params{
     add_snps_to_pile_up_based_on_genotypes_provided = false // #whether we want to add informative snp to pile up in bam to enhance deconvolutions.
 
     encrypt = false
-    write_h5=false
+    write_h5 = true
     remove_work_dir = false
     cellbender_location="${launchDir}/results"
     skip_handover = false

diff --git a/conf/qc.conf b/conf/qc.conf
@@ -11,7 +11,8 @@ params{
         gene_filters{
             description = """Parameters for sample QC prior to merge.
                 Filters are applied to all samples."""
-            genes_exclude = 'IG[HKL][VDJ]|AC233755.*|IGH[GMDEA]|IGKC|IGLC|IGLL|TR[ABGD][CVDJ]' //# this can be a file, rejex pattern or a list of comma separated gene names
+            //# genes_exclude = 'IG[HKL][VDJ]|AC233755.*|IGH[GMDEA]|IGKC|IGLC|IGLL|TR[ABGD][CVDJ]' //# this can be a file, rejex pattern or a list of comma separated gene names
+            genes_exclude = ''
             variable_genes_exclude = "${projectDir}/assets/genes_remove_hvg_v001.tsv" //# list of hvg to still keep if no geenes are needed to be excluded from integration and clustering then please provide: "no_file__genes_exclude_hvg"
             genes_at_least_in_nr_cells = 5 //# keep genes that are expressed in ceirtain amount of cells.
         }

diff --git a/main.nf b/main.nf
@@ -76,7 +76,13 @@ workflow {
 
 workflow WORK_DIR_REMOVAL{
     // This process should be run with caution as it will remove the work directory and copy the results as an actual files
-    RSYNC_RESULTS_REMOVE_WORK_DIR(params.outdir,params.tmpdir)
+
+
+    out_ch = params.outdir
+    ? Channel.fromPath(params.outdir, checkIfExists:true)
+    : Channel.fromPath("${launchDir}/${outdir}")
+
+    RSYNC_RESULTS_REMOVE_WORK_DIR(out_ch,params.tmpdir)
 }
 
 workflow JUST_CELLTYPES{

diff --git a/modules/nf-core/modules/doubletfinder/main.nf b/modules/nf-core/modules/doubletfinder/main.nf
@@ -8,7 +8,7 @@ process DOUBLET_FINDER {
         container "mercury/azimuth_dsb:6_03_2024"
     }
 
-    publishDir  path: "${params.outdir}/multiplet.method=DoubletFinder",
+    publishDir  path: "${params.outdir}/doublets/multiplet.method=DoubletFinder",
                 mode: "${params.copy_mode}",
                 overwrite: "true"
 
@@ -27,7 +27,7 @@ process DOUBLET_FINDER {
 
     script:
 
-        outdir = "${params.outdir}/multiplet"
+        outdir = "${params.outdir}/doublets/multiplet"
         outdir = "${outdir}.method=doubletFinder"
         outfile = "${experiment_id}"