Merge pull request #25 from mskcc/feature/add_pileup_to_copy_outputs

Add pileup to copy outputs

test/copy_outputs.yaml

@@ -1,20 +1,25 @@
 vcf:
-- class: File
-  path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.annotate-variants.vcf
-- class: File
-  path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.annotate-variants.vcf
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.annotate-variants.vcf
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.annotate-variants.vcf
 bam:
-- class: File
-  path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads.bam
-- class: File
-  path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads.bam
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads.bam
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads.bam
 maf:
-- class: File
-  path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.muts.maf
-- class: File
-  path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.muts.maf
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.muts.maf
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.muts.maf
 meta:
-- class: File
-  path: /juno/work/ci/argos-test/data/fastq/DU874145-N/SampleSheet.csv
-- class: File
-  path: /juno/work/ci/argos-test/data/fastq/DU874145-T/SampleSheet.csv
+  - class: File
+    path: /juno/work/ci/argos-test/data/fastq/DU874145-N/SampleSheet.csv
+  - class: File
+    path: /juno/work/ci/argos-test/data/fastq/DU874145-T/SampleSheet.csv
+pileup:
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.rg.md.pileup
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.pileup

test/copy_outputs_without_meta.yaml

@@ -1,15 +1,20 @@
 vcf:
-- class: File
-  path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.annotate-variants.vcf
-- class: File
-  path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.annotate-variants.vcf
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.annotate-variants.vcf
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.annotate-variants.vcf
 bam:
-- class: File
-  path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads.bam
-- class: File
-  path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads.bam
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.abra.printreads.bam
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_normal.rg.md.abra.printreads.bam
 maf:
-- class: File
-  path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.muts.maf
-- class: File
-  path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.muts.maf
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.foo_normal.muts.maf
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair1/PairWorkflow/bar_tumor.bar_normal.muts.maf
+pileup:
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_tumor.rg.md.pileup
+  - class: File
+    path: /juno/work/ci/argos-test/data/PairWorkflowPair0/PairWorkflow/foo_normal.rg.md.pileup

workflows/copy_outputs.cwl

@@ -15,6 +15,7 @@ inputs:
   vcf: File[]
   bam: File[]
   maf: File[]
+  pileup: File[]
   meta:
     type: File[]
     default: []
@@ -30,6 +31,9 @@ outputs:
   maf_dir:
     type: Directory
     outputSource: collect_maf/directory
+  pileup_dir:
+    type: Directory
+    outputSource: collect_pileup/directory
   meta_files:
     type: File[]
     outputSource: meta
@@ -57,4 +61,11 @@ steps:
       output_directory_name:
         valueFrom: ${ return "maf"; }
     out: [directory]
+  collect_pileup:
+    run: ../tools/consolidate-files/consolidate-files.cwl
+    in:
+      files: pileup
+      output_directory_name:
+        valueFrom: ${ return "pileup"; }
+    out: [directory]