force germline workflows to produce genotyped vcf

genome · Jul 13, 2021 · dcefd05 · dcefd05
1 parent f8dff29
commit dcefd05
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Showing 5 changed files with 2 additions and 25 deletions.
diff --git a/definitions/pipelines/germline_exome.cwl b/definitions/pipelines/germline_exome.cwl
@@ -68,10 +68,6 @@ inputs:
         secondaryFiles: [.tbi]
     picard_metric_accumulation_level:
         type: string
-    emit_reference_confidence:
-        type:
-            type: enum
-            symbols: ['NONE', 'BP_RESOLUTION', 'GVCF']
     gvcf_gq_bands:
         type: string[]
     intervals:
@@ -237,7 +233,6 @@ steps:
         in:
             reference: reference
             bam: alignment_and_qc/bam
-            emit_reference_confidence: emit_reference_confidence
             gvcf_gq_bands: gvcf_gq_bands
             intervals: intervals
             ploidy: ploidy

diff --git a/definitions/pipelines/germline_exome_hla_typing.cwl b/definitions/pipelines/germline_exome_hla_typing.cwl
@@ -63,10 +63,6 @@ inputs:
         secondaryFiles: [.tbi]
     picard_metric_accumulation_level:
         type: string
-    emit_reference_confidence:
-        type:
-            type: enum
-            symbols: ['NONE', 'BP_RESOLUTION', 'GVCF']
     gvcf_gq_bands:
         type: string[]
     intervals:
@@ -183,7 +179,6 @@ steps:
             summary_intervals: summary_intervals
             omni_vcf: omni_vcf
             picard_metric_accumulation_level: picard_metric_accumulation_level
-            emit_reference_confidence: emit_reference_confidence
             gvcf_gq_bands: gvcf_gq_bands
             intervals: intervals
             ploidy: ploidy

diff --git a/definitions/pipelines/germline_wgs.cwl b/definitions/pipelines/germline_wgs.cwl
@@ -33,10 +33,6 @@ inputs:
         secondaryFiles: [.tbi]
     picard_metric_accumulation_level:
         type: string
-    emit_reference_confidence:
-        type:
-            type: enum
-            symbols: ['NONE', 'BP_RESOLUTION', 'GVCF']
     gvcf_gq_bands:
         type: string[]
     intervals:
@@ -350,7 +346,6 @@ steps:
         in:
             reference: reference
             bam: alignment_and_qc/bam
-            emit_reference_confidence: emit_reference_confidence
             gvcf_gq_bands: gvcf_gq_bands
             intervals: intervals
             ploidy: ploidy

diff --git a/definitions/pipelines/immuno.cwl b/definitions/pipelines/immuno.cwl
@@ -243,10 +243,6 @@ inputs:
         doc: "An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF"
 
     #germline inputs
-    emit_reference_confidence:
-        type:
-            type: enum
-            symbols: ['NONE', 'BP_RESOLUTION', 'GVCF']
     gvcf_gq_bands:
         type: string[]
     gatk_haplotypecaller_intervals:
@@ -879,7 +875,6 @@ steps:
             summary_intervals: summary_intervals
             omni_vcf: omni_vcf
             picard_metric_accumulation_level: picard_metric_accumulation_level
-            emit_reference_confidence: emit_reference_confidence
             gvcf_gq_bands: gvcf_gq_bands
             intervals: gatk_haplotypecaller_intervals
             ploidy: ploidy

diff --git a/definitions/subworkflows/germline_detect_variants.cwl b/definitions/subworkflows/germline_detect_variants.cwl
@@ -19,10 +19,6 @@ inputs:
     bam:
         type: File
         secondaryFiles: [^.bai]
-    emit_reference_confidence:
-        type:
-            type: enum
-            symbols: ['NONE', 'BP_RESOLUTION', 'GVCF']
     gvcf_gq_bands:
         type: string[]
     intervals:
@@ -101,7 +97,8 @@ steps:
         in:
             reference: reference
             bam: bam
-            emit_reference_confidence: emit_reference_confidence
+            emit_reference_confidence:
+                default: "NONE"
             gvcf_gq_bands: gvcf_gq_bands
             intervals: intervals
             contamination_fraction: contamination_fraction