Updating to allow for two vcfs of known sites

[arvados-tutorial.git] / 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 86d1e1051114ca42f41e956aae55c1d3d9d0028c..76e4798bf270315a57d10a2363aa203487feedc1 100644 (file)
--- 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
@@ -47,18 +56,18 @@ 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 reports
-    format: edam:format_1964 # HTML
+    format: edam:format_2331 # HTML
     outputSource: fastqc/out-html
   qc-zip:
     type: File[]
@@ -72,7 +81,7 @@ outputs:
   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