diff --git a/subworkflows/freebayes.cwl b/subworkflows/freebayes.cwl index fb36248..f320362 100644 --- 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 index 604bc63..dc6418d 100644 --- 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"}