diff --git a/README.md b/README.md index 24ecfa2..d891c44 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -# roslin-cwl +# Argos-cwl -CWLs for the Roslin pipeline. +CWLs for the Argos pipeline. The CWLs are categorized in multiple directories based on their unit of work, although the CWLs contained within can refer to other CWL directories via their relative path. @@ -10,7 +10,7 @@ For example, each CWL module that performs at the tumor-normal pair level are co This repo contains git submodules; make sure to `git clone --recursive` when downloading. -CWLs have been tested with the `toil` executor, found [here](https://github.com/DataBiosphere/toil). +CWLs have been tested with the `toil` executor, found [here](https://github.com/DataBiosphere/toil). ## Directories diff --git a/modules/pair/helix_filters_01 b/modules/pair/helix_filters_01 index 5488b2a..647953d 160000 --- a/modules/pair/helix_filters_01 +++ b/modules/pair/helix_filters_01 @@ -1 +1 @@ -Subproject commit 5488b2ac221311ef012f82d23a271d8a8034f175 +Subproject commit 647953d576fbf60161474a479cf0e88be30c3855 diff --git a/test/copy_outputs.yaml b/test/copy_outputs.yaml index eea5e7f..67ee2ba 100644 --- a/test/copy_outputs.yaml +++ b/test/copy_outputs.yaml @@ -1,35 +1,35 @@ vcf: - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.annotate-variants.vcf + path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.annotate-variants.vcf - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.annotate-variants.vcf + path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.annotate-variants.vcf bam: - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads.bam + path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads.bam - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads.bam + path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads.bam maf: - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.muts.maf + path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.muts.maf - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.muts.maf + path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.muts.maf facets: - normal_id: foo_normal tumor_id: foo_tumor files: - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads__foo_tumor.rg.md.abra.printreads_hisens.CNCF.png + path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads__foo_tumor.rg.md.abra.printreads_hisens.CNCF.png - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads__foo_tumor.rg.md.abra.printreads_purity.CNCF.png + path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads__foo_tumor.rg.md.abra.printreads_purity.CNCF.png - normal_id: bar_normal tumor_id: bar_tumor files: - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_hisens.CNCF.png + path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_hisens.CNCF.png - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_purity.CNCF.png + path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_purity.CNCF.png meta: - class: File - path: /juno/work/ci/roslin-test/data/fastq/DU874145-N/SampleSheet.csv + path: /juno/work/ci/argos-test/data/fastq/DU874145-N/SampleSheet.csv - class: File - path: /juno/work/ci/roslin-test/data/fastq/DU874145-T/SampleSheet.csv \ No newline at end of file + path: /juno/work/ci/argos-test/data/fastq/DU874145-T/SampleSheet.csv \ No newline at end of file diff --git a/test/copy_outputs_without_meta.yaml b/test/copy_outputs_without_meta.yaml index 92ecf4f..7492375 100644 --- a/test/copy_outputs_without_meta.yaml +++ b/test/copy_outputs_without_meta.yaml @@ -1,30 +1,30 @@ vcf: - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.annotate-variants.vcf + path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.annotate-variants.vcf - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.annotate-variants.vcf + path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.annotate-variants.vcf bam: - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads.bam + path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads.bam - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads.bam + path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads.bam maf: - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.muts.maf + path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.muts.maf - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.muts.maf + path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.muts.maf facets: - normal_id: foo_normal tumor_id: foo_tumor files: - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads__foo_tumor.rg.md.abra.printreads_hisens.CNCF.png + path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads__foo_tumor.rg.md.abra.printreads_hisens.CNCF.png - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads__foo_tumor.rg.md.abra.printreads_purity.CNCF.png + path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads__foo_tumor.rg.md.abra.printreads_purity.CNCF.png - normal_id: bar_normal tumor_id: bar_tumor files: - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_hisens.CNCF.png + path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_hisens.CNCF.png - class: File - path: /juno/work/ci/roslin-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_purity.CNCF.png \ No newline at end of file + path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_purity.CNCF.png \ No newline at end of file diff --git a/test/inputs.yaml b/test/inputs.yaml index de710f1..09f3580 100644 --- a/test/inputs.yaml +++ b/test/inputs.yaml @@ -85,7 +85,7 @@ curated_bams: db_files: bait_intervals: class: File - location: /juno/work/ci/resources/roslin_resources/targets/IMPACT468/b37/picard_baits.interval_list + location: /juno/work/ci/resources/genomic_resources/targets/IMPACT468/b37/picard_baits.interval_list conpair_markers: /usr/bin/conpair/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.txt conpair_markers_bed: /usr/bin/conpair/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed custom_enst: /usr/bin/vcf2maf/data/isoform_overrides_at_mskcc @@ -97,33 +97,21 @@ db_files: path: /juno/work/ci/resources/genomes/GRCh37/facets_snps/dbsnp_137.b37__RmDupsClean__plusPseudo50__DROP_SORT.vcf.gz fp_genotypes: class: File - location: /juno/work/ci/resources/roslin_resources/targets/IMPACT468/b37/FP_tiling_genotypes.txt + location: /juno/work/ci/resources/genomic_resources/targets/IMPACT468/b37/FP_tiling_genotypes.txt fp_intervals: class: File - location: /juno/work/ci/resources/roslin_resources/targets/IMPACT468/b37/FP_tiling_intervals.list - grouping_file: - class: File - path: /juno/work/ci/roslin-test/variant/2.6.1/workspace/nikhil-3.10/examples/Alignment/Proj_ROSLIN_DEV_sample_grouping.txt + location: /juno/work/ci/resources/genomic_resources/targets/IMPACT468/b37/FP_tiling_intervals.list hotspot_list: /usr/bin/ngs-filters/data/hotspot-list-union-v1-v2.txt hotspot_list_maf: class: File - path: /juno/work/ci/resources/roslin-qc/hotspot-list-union-v1-v2.maf + path: /juno/work/ci/resources/qc_resources/hotspot-list-union-v1-v2.maf hotspot_vcf: /usr/bin/basicfiltering/data/hotspot-list-union-v1-v2.vcf - mapping_file: - class: File - path: /juno/work/ci/roslin-test/variant/2.6.1/workspace/nikhil-3.10/examples/Alignment/Proj_ROSLIN_DEV_sample_mapping.txt - pairing_file: - class: File - path: /juno/work/ci/roslin-test/variant/2.6.1/workspace/nikhil-3.10/examples/Alignment/Proj_ROSLIN_DEV_sample_pairing.txt refseq: class: File path: /juno/work/ci/resources/request_files/refseq/refGene_b37.sorted.txt - request_file: - class: File - path: /juno/work/ci/roslin-test/variant/2.6.1/workspace/nikhil-3.10/examples/Alignment/Proj_ROSLIN_DEV_request.txt target_intervals: class: File - location: /juno/work/ci/resources/roslin_resources/targets/IMPACT468/b37/picard_targets.interval_list + location: /juno/work/ci/resources/genomic_resources/targets/IMPACT468/b37/picard_targets.interval_list vep_data: /var/cache vep_path: /usr/bin/vep dbsnp: @@ -159,10 +147,10 @@ pairs: group: Group_2 zR1: - class: File - path: /juno/work/ci/roslin-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz + path: /juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz zR2: - class: File - path: /juno/work/ci/roslin-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz + path: /juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz - CN: MSKCC ID: foo_normal LB: foo_normal_1 @@ -177,7 +165,7 @@ pairs: adapter2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT bam: - class: File - path: /juno/work/ci/roslin-test/data/SampleWorkflowPair0Sample1/SampleWorkflow/foo_normal.rg.md.bam + path: /juno/work/ci/argos-test/data/SampleWorkflowPair0Sample1/SampleWorkflow/foo_normal.rg.md.bam bwa_output: foo_normal.bam group: Group_2 zR1: [] @@ -190,10 +178,10 @@ pairs: - bar_tumor_1-bar_tumor R1: - class: File - path: /juno/work/ci/roslin-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz + path: /juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz R2: - class: File - path: /juno/work/ci/roslin-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz + path: /juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz RG_ID: - bar_tumor_1-bar_tumorPE adapter: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG @@ -211,10 +199,10 @@ pairs: - bar_normal_1-bar_normal R1: - class: File - path: /juno/work/ci/roslin-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz + path: /juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz R2: - class: File - path: /juno/work/ci/roslin-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz + path: /juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz RG_ID: - bar_normal_1-bar_normalPE adapter: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG