Merge pull request #17 from kids-first/feature/mb-add-default

✏️ Added defaults
kids-first · May 20, 2024 · 5828407 · 5828407
2 parents f777ca0 + 0d58891
commit 5828407
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Showing 3 changed files with 7 additions and 1 deletion.
diff --git a/tools/bcftools_filter_vcf.cwl b/tools/bcftools_filter_vcf.cwl
@@ -48,7 +48,7 @@ inputs:
   threads: { type: 'int?', default: 4 }
   exclude_expression: { type: 'string?', doc: "See bcftools docs for valid expression. Can't be used at the same time as include_expression.  Use double quotes when a string needs to be quoted"}
   filter_expression: { type: 'string?', doc: "Add values from FILTER field to subset on"}
-  output_type: { type: [ 'null', {type: enum, name: output_type, symbols: [ "u", "b", "v", "z"]}]}
+  output_type: { type: [ 'null', {type: enum, name: output_type, symbols: [ "u", "b", "v", "z"]}], default: "z"}
   sample_name: { type: 'string?', doc: "csv string of samples if user wishes to apply filtering to and output specific samples"}
   output_basename: string
 outputs:

diff --git a/workflows/kfdrc-germline-snv-annot-workflow.cwl b/workflows/kfdrc-germline-snv-annot-workflow.cwl
@@ -204,6 +204,8 @@ requirements:
 - class: ScatterFeatureRequirement
 - class: MultipleInputFeatureRequirement
 - class: SubworkflowFeatureRequirement
+- class: StepInputExpressionRequirement
+- class: InlineJavascriptRequirement
 inputs:
   indexed_reference_fasta: {type: 'File', secondaryFiles: [.fai, ^.dict], "sbg:suggestedValue": {class: File, path: 60639014357c3a53540ca7a3,
       name: Homo_sapiens_assembly38.fasta, secondaryFiles: [{class: File, path: 60639019357c3a53540ca7e7, name: Homo_sapiens_assembly38.dict},
@@ -251,6 +253,8 @@ steps:
       input_vcf: input_vcf
       include_expression: bcftools_prefilter_csv
       output_basename: output_basename
+      output_type:
+        valueFrom: "z"
     out: [filtered_vcf]
 
   normalize_vcf:

diff --git a/workflows/kfdrc-somatic-snv-annot-workflow.cwl b/workflows/kfdrc-somatic-snv-annot-workflow.cwl
@@ -291,6 +291,8 @@ steps:
       input_vcf: hotspots_annotation/hotspots_vcf
       include_expression: bcftools_public_filter
       output_basename: output_basename
+      output_type:
+        valueFrom: "z"
     out: [filtered_vcf]
   kfdrc_vcf2maf_public:
     run: ../tools/kf_mskcc_vcf2maf.cwl