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maca_chr19_samplesheet_skip_umitools_classinput_glm.conf
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/*
* -------------------------------------------------
* Nextflow config file for running tests
* -------------------------------------------------
* Defines bundled input files and everything required
* to run a fast and simple test. Use as follows:
* nextflow run nf-core/sicilian -profile test,<docker/singularity>
*/
params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'
max_cpus = 2
// max_memory = 6.GB
max_time = 48.h
outdir = './results'
// Input data
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
// TODO nf-core: Give any required params for the test so that command line flags are not needed
single_end = false
input = false
skip_umitools = true
skip_star = true
skip_classinput = true
skip_glm = true
input_csv = 'maca_bladder_samplesheet_skip_star_classinput_glm.csv'
star_index = 's3://salzman-lab/nf-sicilian-outputs/aws-maca-small-chr19/genome/index/star/'
fasta = 'https://github.com/czbiohub/test-datasets/raw/olgabot/sicilian/reference/mm10_chrom19.fa'
gtf = 'https://github.com/czbiohub/test-datasets/raw/olgabot/sicilian/reference/GCF_000001635.26_GRCm38.p6_genomic.chr19.gtf.gz'
// star_bam_paths = [
// ['MACA_24m_M_BLADDER_58_S5_L001_T1', ['./results/star/MACA_24m_M_BLADDER_58_S5_L001_T1.Aligned.out.bam']],
// ['MACA_24m_M_BLADDER_58_S5_L002_T1', ['./results/star/MACA_24m_M_BLADDER_58_S5_L002_T1.Aligned.out.bam']],
// ['MACA_24m_M_BLADDER_59_S6_L002_T1', ['./results/star/MACA_24m_M_BLADDER_59_S6_L002_T1.Aligned.out.bam']],
// ['MACA_24m_M_BLADDER_60_S12_L001_T1', ['./results/star/MACA_24m_M_BLADDER_60_S12_L001_T1.Aligned.out.bam']],
// ['MACA_24m_M_BLADDER_60_S12_L002_T1', ['./results/star/MACA_24m_M_BLADDER_60_S12_L002_T1.Aligned.out.bam']],
// ]
// star_sj_out_tab_paths = [
// ['MACA_24m_M_BLADDER_58_S5_L001_T1', ['./results/star/log/MACA_24m_M_BLADDER_58_S5_L001_T1.SJ.out.tab']],
// ['MACA_24m_M_BLADDER_58_S5_L002_T1', ['./results/star/log/MACA_24m_M_BLADDER_58_S5_L002_T1.SJ.out.tab']],
// ['MACA_24m_M_BLADDER_59_S6_L002_T1', ['./results/star/log/MACA_24m_M_BLADDER_59_S6_L002_T1.SJ.out.tab']],
// ['MACA_24m_M_BLADDER_60_S12_L001_T1', ['./results/star/log/MACA_24m_M_BLADDER_60_S12_L001_T1.SJ.out.tab']],
// ['MACA_24m_M_BLADDER_60_S12_L002_T1', ['./results/star/log/MACA_24m_M_BLADDER_60_S12_L002_T1.SJ.out.tab']],
// ]
// star_reads_per_gene_paths = [
// ['MACA_24m_M_BLADDER_58_S5_L001_T1', ['./results/star/log/MACA_24m_M_BLADDER_58_S5_L001_T1.ReadsPerGene.out.tab']],
// ['MACA_24m_M_BLADDER_58_S5_L002_T1', ['./results/star/log/MACA_24m_M_BLADDER_58_S5_L002_T1.ReadsPerGene.out.tab']],
// ['MACA_24m_M_BLADDER_59_S6_L002_T1', ['./results/star/log/MACA_24m_M_BLADDER_59_S6_L002_T1.ReadsPerGene.out.tab']],
// ['MACA_24m_M_BLADDER_60_S12_L001_T1', ['./results/star/log/MACA_24m_M_BLADDER_60_S12_L001_T1.ReadsPerGene.out.tab']],
// ['MACA_24m_M_BLADDER_60_S12_L002_T1', ['./results/star/log/MACA_24m_M_BLADDER_60_S12_L002_T1.ReadsPerGene.out.tab']],
// ]
// star_chimeric_junction_paths = [
// ['MACA_24m_M_BLADDER_58_S5_L001_T1', ['./results/star/log/MACA_24m_M_BLADDER_58_S5_L001_T1.Chimeric.out.junction']],
// ['MACA_24m_M_BLADDER_58_S5_L002_T1', ['./results/star/log/MACA_24m_M_BLADDER_58_S5_L002_T1.Chimeric.out.junction']],
// ['MACA_24m_M_BLADDER_59_S6_L002_T1', ['./results/star/log/MACA_24m_M_BLADDER_59_S6_L002_T1.Chimeric.out.junction']],
// ['MACA_24m_M_BLADDER_60_S12_L001_T1', ['./results/star/log/MACA_24m_M_BLADDER_60_S12_L001_T1.Chimeric.out.junction']],
// ['MACA_24m_M_BLADDER_60_S12_L002_T1', ['./results/star/log/MACA_24m_M_BLADDER_60_S12_L002_T1.Chimeric.out.junction']],
// ]
// sicilian_class_input_paths = [
// ['MACA_24m_M_BLADDER_58_S5_L001_T1', ['./results/sicilian/class_input/MACA_24m_M_BLADDER_58_S5_L001_T1__class_input.tsv']],
// ['MACA_24m_M_BLADDER_58_S5_L002_T1', ['./results/sicilian/class_input/MACA_24m_M_BLADDER_58_S5_L002_T1__class_input.tsv']],
// ['MACA_24m_M_BLADDER_59_S6_L002_T1', ['./results/sicilian/class_input/MACA_24m_M_BLADDER_59_S6_L002_T1__class_input.tsv']],
// ['MACA_24m_M_BLADDER_60_S12_L001_T1', ['./results/sicilian/class_input/MACA_24m_M_BLADDER_60_S12_L001_T1__class_input.tsv']],
// ['MACA_24m_M_BLADDER_60_S12_L002_T1', ['./results/sicilian/class_input/MACA_24m_M_BLADDER_60_S12_L002_T1__class_input.tsv']],
// ]
// sicilian_glm_output_paths = [
// ['MACA_24m_M_BLADDER_58_S5_L001_T1', ['./results/sicilian/glm/glm_output/MACA_24m_M_BLADDER_58_S5_L001_T1__GLM_output.txt']],
// ['MACA_24m_M_BLADDER_58_S5_L002_T1', ['./results/sicilian/glm/glm_output/MACA_24m_M_BLADDER_58_S5_L002_T1__GLM_output.txt']],
// ['MACA_24m_M_BLADDER_59_S6_L002_T1', ['./results/sicilian/glm/glm_output/MACA_24m_M_BLADDER_59_S6_L002_T1__GLM_output.txt']],
// ['MACA_24m_M_BLADDER_60_S12_L001_T1', ['./results/sicilian/glm/glm_output/MACA_24m_M_BLADDER_60_S12_L001_T1__GLM_output.txt']],
// ['MACA_24m_M_BLADDER_60_S12_L002_T1', ['./results/sicilian/glm/glm_output/MACA_24m_M_BLADDER_60_S12_L002_T1__GLM_output.txt']],
// ]
domain = 's3://salzman-lab/hg38_ref_files/domain_file.txt'
save_reference = true
stranded = true
tenx = true
annotator = 'https://github.com/czbiohub/test-datasets/raw/olgabot/sicilian/reference/sicilian/GCF_000001635_gene_names.pkl'
exon_bounds = 'https://github.com/czbiohub/test-datasets/raw/olgabot/sicilian/reference/sicilian/GCF_000001635_exon_bounds.pkl'
splices = 'https://github.com/czbiohub/test-datasets/raw/olgabot/sicilian/reference/sicilian/GCF_000001635_splices.pkl'
// Ignore `--input` as otherwise the parameter validation will throw an error
schema_ignore_params = 'genomes,input_paths,input,sicilian_glm_output_paths,sicilian_class_input_paths,star_chimeric_junction_paths,star_reads_per_gene_paths,star_sj_out_tab_paths,star_bam_paths'
}
process {
executor = 'awsbatch'
queue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036'
errorStrategy = { task.exitStatus in [143,137,104,134,139,160] ? 'retry' : 'finish' }
maxRetries = 1
}
tower {
endpoint = 'http://nftower.czbiohub.org:8000/api'
enabled = true
}