Updating to allow for two vcfs of known sites

[arvados-tutorial.git] / WGS-processing / cwl / wgs-processing-wf.cwl

diff --git a/WGS-processing/cwl/wgs-processing-wf.cwl b/WGS-processing/cwl/wgs-processing-wf.cwl
index 58e38cbf2d6453908bfb5b4c4564daa439996988..8499b92bdbedbc119abc8dd45dab04a39b827703 100644 (file)
--- a/WGS-processing/cwl/wgs-processing-wf.cwl
+++ b/WGS-processing/cwl/wgs-processing-wf.cwl
@@ -22,12 +22,20 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  knownsites:
+  fullintervallist:
+    type: File
+  knownsites1:
+    type: File
+    format: edam:format_3016 # VCF
+    label: VCF of known SNPS sites for BQSR
+    secondaryFiles:
+      - .idx   
+  knownsites2:
     type: File
     format: edam:format_3016 # VCF
-    label: VCF of known polymorphic sites for BQSR
+    label: VCF of known indel sites for BQSR
     secondaryFiles:
-      - .tbi   
+      - .tbi
   scattercount: 
     type: string
     label: Desired split for variant calling
@@ -40,11 +48,11 @@ 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:
@@ -53,11 +61,10 @@ outputs:
     outputSource: bwamem-gatk-report/gvcf
     format: edam:format_3016 # GVCF
     label: GVCFs generated from GATK 
-    
   report:
     type: File[]  
     outputSource: bwamem-gatk-report/report
-    format: edam:format_1964 # HTML
+    format: edam:format_2331 # HTML
     label: ClinVar variant reports 
 
 steps:
@@ -75,8 +82,10 @@ steps:
       fastq1: getfastq/fastq1
       fastq2: getfastq/fastq2
       reference: reference
+      fullintervallist: fullintervallist
       sample: getfastq/sample
-      knownsites: knownsites
+      knownsites1: knownsites1
+      knownsites2: knownsites2
       scattercount: scattercount
       clinvarvcf: clinvarvcf
       reportfunc: reportfunc
@@ -91,6 +100,6 @@ $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