Merge pull request #4 from mskcc/develop

Develop
mskcc · May 21, 2020 · 2fc732c · 2fc732c
2 parents 4034144 + 098061e
commit 2fc732c
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diff --git 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
diff --git 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
+  path: /juno/work/ci/argos-test/data/fastq/DU874145-T/SampleSheet.csv
diff --git 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
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads__bar_tumor.rg.md.abra.printreads_purity.CNCF.png
diff --git 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
+3 −0		.gitignore
+32 −10		Makefile
+8 −0		README.md
+17 −0		cwl/cat.cwl
+39 −14		cwl/concat.cwl
+22 −0		cwl/head.cwl
+5 −5		cwl/maf_filter.cwl
+22 −0		cwl/tail.cwl
+8 −7		cwl/workflow.cwl
+88 −88		ref/roslin_resources.json
+17 −0		test.py
+0 −0		tests/__init__.py
+35 −0		tests/settings.py
+472 −0		tests/test_concat.py
+143 −0		tests/test_copy_number.py
+245 −0		tests/test_maf_filter.py
+110 −0		tests/test_put_in_dir.py
+240 −0		tests/test_workflow.py
+20 −0		tests/tools.py