Updating to allow for two vcfs of known sites

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

diff --git a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
index dbb1d5024731aa1923fa539217264e6a7070600c..76e4798bf270315a57d10a2363aa203487feedc1 100644 (file)
--- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@ -32,12 +32,18 @@ inputs:
   sample: 
     type: string
     label: Sample Name
-  knownsites:
+  knownsites1:
     type: File
     format: edam:format_3016 # VCF
     label: VCF of known polymorphic sites for BQSR
     secondaryFiles:
-      - .tbi   
+      - .idx 
+  knownsites2:
+    type: File
+    format: edam:format_3016 # VCF
+    label: VCF of known polymorphic sites for BQSR
+    secondaryFiles:
+      - .tbi  
   scattercount: 
     type: string
     label: Desired split for variant calling
@@ -117,7 +123,8 @@ steps:
       bam: samtools-index/indexedbam
       sample: sample
       scattercount: scattercount
-      knownsites: knownsites
+      knownsites1: knownsites1
+      knownsites2: knownsites2
     out: [gatheredgvcf]
   generate-report:
     run: report-wf.cwl

diff --git a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
index 7ae08377f143563bd425ed4314d4b7af8d5a8d39..2de30a62b88d0a0923b6951eaa05b9cf31c0ddc2 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
@@ -41,7 +41,13 @@ inputs:
   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
@@ -69,7 +75,9 @@ arguments:
   - prefix: "-I"
     valueFrom: $(inputs.bam)
   - prefix: "--known-sites"
-    valueFrom: $(inputs.knownsites)
+    valueFrom: $(inputs.knownsites1)
+  - prefix: "--known-sites"
+    valueFrom: $(inputs.knownsites2)
   - prefix: "-L"
     valueFrom: $(inputs.intervallist)
   - prefix: "-O"

diff --git a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
index de4a648e8a90cd08a697203e205e931a95be8b1c..d9023c92186ca6fda034cbf4552accdb5c069364 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@ -27,7 +27,13 @@ inputs:
   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
@@ -51,7 +57,8 @@ steps:
       bam: bam
       reference: reference
       sample: sample
-      knownsites: knownsites
+      knownsites1: knownsites1
+      knownsites2: knownsites2
       intervallist: intervallist
     out: [recaltable]
   applyBQSR:

diff --git a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
index 80d7601115c8ef2cb1839e273266cdc1947ce4dd..13bd4af04c3528e384078e073c4e722823e498ec 100644 (file)
--- a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
@@ -31,7 +31,13 @@ inputs:
   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
@@ -67,7 +73,8 @@ steps:
       bam: bam
       reference: reference
       sample: sample
-      knownsites: knownsites
+      knownsites1: knownsites1
+      knownsites2: knownsites2
       intervallist: splitintervals/intervalfiles
     out: [gvcf]
 

diff --git a/WGS-processing/cwl/wgs-processing-wf.cwl b/WGS-processing/cwl/wgs-processing-wf.cwl
index 8cbcf5ee03b17f7d5800b611fd29a4d69cfcc105..8499b92bdbedbc119abc8dd45dab04a39b827703 100644 (file)
--- a/WGS-processing/cwl/wgs-processing-wf.cwl
+++ b/WGS-processing/cwl/wgs-processing-wf.cwl
@@ -24,12 +24,18 @@ inputs:
       - ^.dict
   fullintervallist:
     type: File
-  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
@@ -78,7 +84,8 @@ steps:
       reference: reference
       fullintervallist: fullintervallist
       sample: getfastq/sample
-      knownsites: knownsites
+      knownsites1: knownsites1
+      knownsites2: knownsites2
       scattercount: scattercount
       clinvarvcf: clinvarvcf
       reportfunc: reportfunc

diff --git a/WGS-processing/yml/wgs-processing-wf.yml b/WGS-processing/yml/wgs-processing-wf.yml
index 299a674eaa08056538c86d0745dabd6e80dea04f..49ac46d80ed6440bc6c9fa84019b31130c7f46d8 100644 (file)
--- a/WGS-processing/yml/wgs-processing-wf.yml
+++ b/WGS-processing/yml/wgs-processing-wf.yml
@@ -32,7 +32,12 @@ tailhtml:
 
 scattercount: '20'
 
-knownsites:
+knownsites1:
+  class: File
+  format: edam:format_3016
+  location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.dbsnp138.vcf 
+
+knownsites2:
   class: File
   format: edam:format_3016
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz