Merge pull request #46 from kids-first/bug/mb-update-refs

🧹 rm no longer needed clinvar defaults
kids-first · May 21, 2024 · e9562ca · e9562ca
2 parents 0bf0609 + 717a43a
commit e9562ca
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diff --git a/subworkflows/freebayes.cwl b/subworkflows/freebayes.cwl
@@ -26,7 +26,7 @@ inputs:
 
   # Annotation
   bcftools_annot_clinvar_columns: {type: 'string?', doc: "csv string of columns from annotation to port into the input vcf", default: "INFO/ALLELEID,INFO/CLNDN,INFO/CLNDNINCL,INFO/CLNDISDB,INFO/CLNDISDBINCL,INFO/CLNHGVS,INFO/CLNREVSTAT,INFO/CLNSIG,INFO/CLNSIGCONF,INFO/CLNSIGINCL,INFO/CLNVC,INFO/CLNVCSO,INFO/CLNVI"}
-  clinvar_annotation_vcf: {type: 'File?', secondaryFiles: ['.tbi'], doc: "additional bgzipped annotation vcf file", "sbg:suggestedValue": {class: File, path: 64e4c9732031aa7ce01f86bf, name: clinvar_20220507_chr_fixed.vcf.gz, secondaryFiles: [{class: File, path: 64e4c97c78c25c546eaa2573, name: clinvar_20220507_chr_fixed.vcf.gz.tbi}]}}
+  clinvar_annotation_vcf: {type: 'File?', secondaryFiles: ['.tbi']}
   echtvar_anno_zips: { type: 'File[]?', doc: "Annotation ZIP files for echtvar anno",
     "sbg:suggestedValue": [{class: File, path: 65c64d847dab7758206248c6, name: gnomad.v3.1.1.custom.echtvar.zip}] } 
   # VEP-specific

diff --git a/workflows/kfdrc-germline-variant-wf.cwl b/workflows/kfdrc-germline-variant-wf.cwl
@@ -355,8 +355,7 @@ inputs:
       the program to group variants into a smaller number of clusters, which results in more variants per cluster."}
   bcftools_annot_clinvar_columns: {type: 'string?', doc: "csv string of columns from annotation to port into the input vcf", default: "INFO/ALLELEID,INFO/CLNDN,INFO/CLNDNINCL,INFO/CLNDISDB,INFO/CLNDISDBINCL,INFO/CLNHGVS,INFO/CLNREVSTAT,INFO/CLNSIG,INFO/CLNSIGCONF,INFO/CLNSIGINCL,INFO/CLNVC,INFO/CLNVCSO,INFO/CLNVI"}
   clinvar_annotation_vcf: {type: 'File?', secondaryFiles: [{pattern: '.tbi', required: true}], doc: "additional bgzipped annotation
-      vcf file", "sbg:suggestedValue": {class: File, path: 64e4c9732031aa7ce01f86bf, name: clinvar_20220507_chr_fixed.vcf.gz, secondaryFiles: [
-        {class: File, path: 64e4c97c78c25c546eaa2573, name: clinvar_20220507_chr_fixed.vcf.gz.tbi}]}}
+      vcf file"}
   echtvar_anno_zips: {type: 'File[]?', doc: "Annotation ZIP files for echtvar anno", "sbg:suggestedValue": [{class: File, path: 65c64d847dab7758206248c6,
         name: gnomad.v3.1.1.custom.echtvar.zip}]}
   vep_buffer_size: {type: 'int?', default: 100000, doc: "Increase or decrease to balance speed and memory usage"}