put report in its own dir

cwl/samples_fillout_index_batch_workflow.cwl

@@ -5,6 +5,16 @@ class: Workflow
 doc: "
 Wrapper to run bam indexing on all bams before submitting for samples fillout
 Also includes steps to pre-filter some maf input files
+
+NOTE: each sample in a sample_group must have a .bam file,
+and there must be a minumum of 1 .maf file amoungst samples in the same sample_group
+this means that for each sample in the sample_group, a .bam is required but a .maf is optional
+as long as one sample in the group has a .maf
+this also means that singleton sample groups, or a sample group with only one sample, MUST
+include a .maf file; singletons cannot lack a .maf
+
+NOTE: all .maf files must be valid, at a minimum they must have a header and at least one variant
+if a sample has no variants in its .maf file, or has an empty .maf file, then it should NOT have a maf_file entry associated with it
 "
 requirements:
   - class: MultipleInputFeatureRequirement

cwl/workflow_with_facets.cwl

@@ -521,11 +521,13 @@ steps:
       portal_meta_fusions_file, # meta_fusions.txt
       portal_meta_mutations_extended_file, # meta_mutations_extended.txt
       portal_meta_cna_segments_file, # <project_id>_meta_cna_hg19_seg.txt
+      portal_meta_sv_file, # meta_SV.txt
       portal_cna_data_file, # data_CNA.txt
       portal_cna_ascna_file, # data_CNA.ascna.txt
       portal_muts_file, # data_mutations_extended.txt
       portal_hisens_segs, # <project_id>_data_cna_hg19.seg
       portal_fusions_data_file, # data_fusions.txt
+      portal_sv_data_file, # data_SV.txt
       portal_case_list_dir,
       portal_report
       ]
@@ -570,13 +572,14 @@ steps:
       portal_meta_fusions_file: run_portal_workflow/portal_meta_fusions_file # meta_fusions.txt
       portal_meta_mutations_extended_file: run_portal_workflow/portal_meta_mutations_extended_file # meta_mutations_extended.txt
       portal_meta_cna_segments_file: run_portal_workflow/portal_meta_cna_segments_file  # <project_id>_meta_cna_hg19_seg.txt
+      portal_meta_sv_file: run_portal_workflow/portal_meta_sv_file # meta_SV.txt
       portal_cna_data_file: run_portal_workflow/portal_cna_data_file # data_CNA.txt
+      portal_sv_data_file: run_portal_workflow/portal_sv_data_file # data_SV.txt
       portal_cna_ascna_file: run_portal_workflow/portal_cna_ascna_file # data_CNA.ascna.txt
       portal_muts_file: merge_maf/output_file # data_mutations_extended.txt
       portal_hisens_segs: run_portal_workflow/portal_hisens_segs # # <project_id>_data_cna_hg19.seg
       portal_fusions_data_file: run_portal_workflow/portal_fusions_data_file # data_fusions.txt
       portal_case_list_dir: run_portal_workflow/portal_case_list_dir
-      portal_report: run_portal_workflow/portal_report
       output_directory_name:
         valueFrom: ${ return "portal"; }
       files:
@@ -590,13 +593,14 @@ steps:
           inputs.portal_meta_fusions_file,
           inputs.portal_meta_mutations_extended_file,
           inputs.portal_meta_cna_segments_file,
+          inputs.portal_meta_sv_file,
+          inputs.portal_sv_data_file,
           inputs.portal_cna_data_file,
           inputs.portal_cna_ascna_file,
           inputs.portal_muts_file,
           inputs.portal_hisens_segs,
           inputs.portal_fusions_data_file,
           inputs.portal_case_list_dir,
-          inputs.portal_report
           ]}
     out: [ directory ]
 
@@ -627,6 +631,19 @@ steps:
           ]}
     out: [ directory ]
 
+  make_reports_dir:
+    doc:
+    run: put_DirFileList_in_dir.cwl
+    in:
+      portal_report: run_portal_workflow/portal_report
+      output_directory_name:
+        valueFrom: ${ return "reports"; }
+      files:
+        valueFrom: ${return [
+          inputs.portal_report
+          ]}
+    out: [ directory ]
+
   make_facets_dir:
     doc: make a single directory to hold the results for all Facets sample pair
     in:
@@ -703,3 +720,7 @@ outputs:
   tmb_dir:
     type: Directory
     outputSource: make_tmb_dir/directory
+
+  reports_dir:
+      type: Directory
+      outputSource: make_reports_dir/directory