X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/611c455f8a94ab5dbd5c94415802b5c7fd009ffc..c604c42bb92a6301b13a250582eabed509adaae1:/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 ee8ae4f..41c9130 100644
--- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@ -3,7 +3,7 @@ class: Workflow
 label: WGS processing workflow for single sample
 
 requirements:
-  - class: SubworkflowFeatureRequirement
+  SubworkflowFeatureRequirement: {}
 
 inputs:
   fastq1:
@@ -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
+    label: VCF of known SNPS sites for BQSR
     secondaryFiles:
-      - .tbi   
+      - .idx
+  knownsites2:
+    type: File
+    format: edam:format_3016 # VCF
+    label: VCF of known indel sites for BQSR
+    secondaryFiles:
+      - .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:
@@ -110,16 +119,18 @@ steps:
     run: scatter-gatk-wf-with-interval.cwl 
     in:
       reference: reference
+      fullintervallist: fullintervallist
       bam: samtools-index/indexedbam
       sample: sample
       scattercount: scattercount
-      knownsites: 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
@@ -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