Merge pull request #25 from kids-first/bug/fix_secondary_file_ref

🔧 Bug/fix secondary file ref
kids-first · Sep 29, 2022 · e39dde7 · e39dde7
2 parents 2b6822c + e9309f2
commit e39dde7
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Showing 2 changed files with 15 additions and 6 deletions.
diff --git a/workflows/kfdrc-germline-snv-annot-workflow.cwl b/workflows/kfdrc-germline-snv-annot-workflow.cwl
@@ -195,7 +195,7 @@ doc: |-
         class: File, path: 632a2b417535110eb78312a5, name: CADDv1.6-38-gnomad.genomes.r3.0.indel.tsv.gz.tbi}]}}
     cadd_snvs: { type: 'File?', secondaryFiles: [.tbi], doc: "VEP-formatted plugin file and index containing CADD SNV annotations", "sbg:suggestedValue": {
         class: File, path: 632a2b417535110eb78312a4, name: CADDv1.6-38-whole_genome_SNVs.tsv.gz, secondaryFiles: [{
-        class: File, path: 632a2b417535110eb78312a5, name: CADDv1.6-38-whole_genome_SNVs.tsv.gz.tbi}]} }
+        class: File, path: 632a2b417535110eb78312a3, name: CADDv1.6-38-whole_genome_SNVs.tsv.gz.tbi}]} }
     intervar: { type: 'File?', doc: "Intervar vcf-formatted file. Exonic SNVs only - for more comprehensive run InterVar. See docs for custom build instructions", secondaryFiles: [.tbi], "sbg:suggestedValue": {
             class: File, path: 633348619968f3738e4ec4b5, name: Exons.all.hg38.intervar.2021-07-31.vcf.gz, secondaryFiles: [{
             class: File, path: 633348619968f3738e4ec4b6, name: Exons.all.hg38.intervar.2021-07-31.vcf.gz.tbi}]} }
@@ -216,7 +216,7 @@ inputs:
         {class: File, path: 60639016357c3a53540ca7af, name: Homo_sapiens_assembly38.fasta.fai}]}}
   input_vcf: {type: 'File', secondaryFiles: ['.tbi'], doc: "Input vcf to annotate"}
   output_basename: string
-  tool_name: string
+  tool_name: { type: string, doc: "File name string suffx to use for output files" }
 
   bcftools_prefilter_csv: {type: 'string?', doc: "csv of bcftools filter params if\
       \ you want to prefilter before annotation"}
@@ -265,7 +265,7 @@ inputs:
   cadd_snvs: {type: 'File?', secondaryFiles: [.tbi], doc: "VEP-formatted plugin file\
       \ and index containing CADD SNV annotations", "sbg:suggestedValue": {class: File,
       path: 632a2b417535110eb78312a4, name: CADDv1.6-38-whole_genome_SNVs.tsv.gz,
-      secondaryFiles: [{class: File, path: 632a2b417535110eb78312a5, name: CADDv1.6-38-whole_genome_SNVs.tsv.gz.tbi}]}}
+      secondaryFiles: [{class: File, path: 632a2b417535110eb78312a3, name: CADDv1.6-38-whole_genome_SNVs.tsv.gz.tbi}]}}
   intervar: {type: 'File?', doc: "Intervar vcf-formatted file. Exonic SNVs only -\
       \ for more comprehensive run InterVar. See docs for custom build instructions",
     secondaryFiles: [.tbi], "sbg:suggestedValue": {class: File, path: 633348619968f3738e4ec4b5,
@@ -369,5 +369,14 @@ steps:
           \ var pro_tbi=self[0] + '.' + self[1] + '.norm.annot.vcf.gz.tbi'; return\
           \ [pro_vcf, pro_tbi];}"
     out: [renamed_files]
+
+$namespaces:
+  sbg: https://sevenbridges.com
+
 sbg:license: Apache License 2.0
 sbg:publisher: KFDRC
+
+"sbg:links":
+- id: 'https://github.com/kids-first/kf-germline-workflow/releases/tag/v0.4.1'
+  label: github-release
+
diff --git a/workflows/kfdrc-single-sample-genotyping-wf.cwl b/workflows/kfdrc-single-sample-genotyping-wf.cwl
@@ -106,7 +106,7 @@ inputs:
       \ the max-Gaussians forces the program to group variants into a smaller number\
       \ of clusters, which results in more variants per cluster."}
   output_basename: string
-  tool_name: string
+  tool_name: { type: 'string?', default: "CGP.filtered.deNovo.vep", doc: "File name string suffx to use for output files" }
   # Annotation
   bcftools_annot_gnomad_columns: {type: 'string?', doc: "csv string of columns from\
       \ annotation to port into the input vcf, i.e", default: "INFO/gnomad_3_1_1_AC:=INFO/AC,INFO/gnomad_3_1_1_AN:=INFO/AN,INFO/gnomad_3_1_1_AF:=INFO/AF,INFO/gnomad_3_1_1_nhomalt:=INFO/nhomalt,INFO/gnomad_3_1_1_AC_popmax:=INFO/AC_popmax,INFO/gnomad_3_1_1_AN_popmax:=INFO/AN_popmax,INFO/gnomad_3_1_1_AF_popmax:=INFO/AF_popmax,INFO/gnomad_3_1_1_nhomalt_popmax:=INFO/nhomalt_popmax,INFO/gnomad_3_1_1_AC_controls_and_biobanks:=INFO/AC_controls_and_biobanks,INFO/gnomad_3_1_1_AN_controls_and_biobanks:=INFO/AN_controls_and_biobanks,INFO/gnomad_3_1_1_AF_controls_and_biobanks:=INFO/AF_controls_and_biobanks,INFO/gnomad_3_1_1_AF_non_cancer:=INFO/AF_non_cancer,INFO/gnomad_3_1_1_primate_ai_score:=INFO/primate_ai_score,INFO/gnomad_3_1_1_splice_ai_consequence:=INFO/splice_ai_consequence"}
@@ -144,7 +144,7 @@ inputs:
   cadd_snvs: {type: 'File?', secondaryFiles: [.tbi], doc: "VEP-formatted plugin file\
       \ and index containing CADD SNV annotations", "sbg:suggestedValue": {class: File,
       path: 632a2b417535110eb78312a4, name: CADDv1.6-38-whole_genome_SNVs.tsv.gz,
-      secondaryFiles: [{class: File, path: 632a2b417535110eb78312a5, name: CADDv1.6-38-whole_genome_SNVs.tsv.gz.tbi}]}}
+      secondaryFiles: [{class: File, path: 632a2b417535110eb78312a3, name: CADDv1.6-38-whole_genome_SNVs.tsv.gz.tbi}]}}
   intervar: {type: 'File?', doc: "Intervar vcf-formatted file. Exonic SNVs only -\
       \ for more comprehensive run InterVar. See docs for custom build instructions",
     secondaryFiles: [.tbi], "sbg:suggestedValue": {class: File, path: 633348619968f3738e4ec4b5,
@@ -362,5 +362,5 @@ hints:
 - VCF
 - VEP
 "sbg:links":
-- id: 'https://github.com/kids-first/kf-germline-workflow/releases/tag/v0.4.0'
+- id: 'https://github.com/kids-first/kf-germline-workflow/releases/tag/v0.4.1'
   label: github-release