X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/4bb5fb748cbceab1f23d3972cd502e94711fc7c9..814e2840b16acbe0e52e6fb3095a87b33269dc50:/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl

diff --git a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
index f1cfad4..76e4798 100644
--- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@ -3,14 +3,14 @@ class: Workflow
 label: WGS processing workflow for single sample
 
 requirements:
-  - class: SubworkflowFeatureRequirement
+  SubworkflowFeatureRequirement: {}
 
 inputs:
-  fastq1: 
+  fastq1:
     type: File
     format: edam:format_1930 # FASTQ
     label: One of set of pair-end FASTQs (R1)
-  fastq2: 
+  fastq2:
     type: File
     format: edam:format_1930 # FASTQ
     label: One of set of pair-end FASTQs (R2)
@@ -26,15 +26,24 @@ inputs:
       - .sa
       - .fai
       - ^.dict
+  fullintervallist:
+    type: File
+    label: Full list of intervals to operate over
   sample: 
     type: string
     label: Sample Name
-  knownsites:
+  knownsites1:
+    type: File
+    format: edam:format_3016 # VCF
+    label: VCF of known polymorphic sites for BQSR
+    secondaryFiles:
+      - .idx 
+  knownsites2:
     type: File
     format: edam:format_3016 # VCF
     label: VCF of known polymorphic sites for BQSR
     secondaryFiles:
-      - .tbi   
+      - .tbi  
   scattercount: 
     type: string
     label: Desired split for variant calling
@@ -47,32 +56,32 @@ inputs:
     label: Function used to create HTML report
   headhtml:
     type: File
-    format: edam:format_1964 # HTML
+    format: edam:format_2331 # HTML
     label: Header for HTML report
   tailhtml:
     type: File
-    format: edam:format_1964 # HTML
+    format: edam:format_2331 # HTML
     label: Footer for HTML report
 
 outputs:
   qc-html:
     type: File[]
-    label: FASTQ QC report
-    format: edam:format_1964 # HTML
+    label: FASTQ QC reports
+    format: edam:format_2331 # HTML
     outputSource: fastqc/out-html
   qc-zip:
     type: File[]
-    label: Zip file of FASTQ QC report and associated data
+    label: Zip files of FASTQ QC report and associated data
     outputSource: fastqc/out-zip 
   gvcf:
     type: File
     outputSource: haplotypecaller/gatheredgvcf
     format: edam:format_3016 # GVCF
-    label: GVCF generated from GATK 
+    label: GVCF generated from GATK Haplotype Caller
   report:
     type: File  
     outputSource: generate-report/report
-    format: edam:format_1964 # HTML
+    format: edam:format_2331 # HTML
     label: ClinVar variant report
 
 steps:
@@ -91,7 +100,7 @@ steps:
       sample: sample
     out: [bam]
   samtools-sort:
-    run: samtools-sort.cwl 
+    run: samtools-sort.cwl
     in:
       bam: bwamem-samtools-view/bam
       sample: sample
@@ -110,21 +119,23 @@ steps:
     run: scatter-gatk-wf-with-interval.cwl 
     in:
       reference: reference
+      fullintervallist: fullintervallist
       bam: samtools-index/indexedbam
       sample: sample
       scattercount: scattercount
-      knownsites1: knownsites
+      knownsites1: knownsites1
+      knownsites2: knownsites2
     out: [gatheredgvcf]
   generate-report:
     run: report-wf.cwl
     in:
       gvcf: haplotypecaller/gatheredgvcf
-      samplename: sample
+      sample: sample
       clinvarvcf: clinvarvcf
       reportfunc: reportfunc
       headhtml: headhtml
       tailhtml: tailhtml
-    out: [report] 
+    out: [report]
 
 s:codeRepository: https://github.com/arvados/arvados-tutorial
 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
@@ -133,6 +144,6 @@ $namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/
 
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl