Switching variable knownsites1 to knownsites

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 86d1e1051114ca42f41e956aae55c1d3d9d0028c..56efe6545d928b4fafdb6b79bce6f8a821761e44 100644 (file)
--- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@ -113,7 +113,7 @@ steps:
       bam: samtools-index/indexedbam
       sample: sample
       scattercount: scattercount
-      knownsites1: knownsites
+      knownsites: knownsites
     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 7e5bf4df4bc863807a4136547ab794af374cb69e..6df9de12675d1a00af561adb2d874376c9cf4801 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
@@ -44,7 +44,7 @@ inputs:
   sample:
     type: string
     label: Sample Name
-  knownsites1: 
+  knownsites: 
     type: File
     format: edam:format_3016 # VCF
     label: VCF of known polymorphic sites for BQSR
@@ -72,7 +72,7 @@ arguments:
   - prefix: "-I"
     valueFrom: $(inputs.bam.basename)
   - prefix: "--known-sites"
-    valueFrom: $(inputs.knownsites1)
+    valueFrom: $(inputs.knownsites)
   - 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 cf815a5178cb9ab03c769f5acc11de7fe5f8fd8e..38e185d5b67e26f299bb39a4b1419cd5893fd9e8 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@ -27,7 +27,7 @@ inputs:
   sample: 
     type: string
     label: Sample Name
-  knownsites1:
+  knownsites:
     type: File
     format: edam:format_3016 # VCF
     label: VCF of known polymorphic sites for BQSR
@@ -51,7 +51,7 @@ steps:
       bam: bam
       reference: reference
       sample: sample
-      knownsites1: knownsites1
+      knownsites: knownsites
       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 45653db5fb11364034e3ead3a1c5d8fc508afe3b..2cf48b5f3943b319885af8d207ee43fc02147f0f 100644 (file)
--- a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
@@ -28,7 +28,7 @@ inputs:
   sample: 
     type: string
     label: Sample Name
-  knownsites1:
+  knownsites:
     type: File
     format: edam:format_3016 # VCF
     label: VCF of known polymorphic sites for BQSR
@@ -63,7 +63,7 @@ steps:
       bam: bam
       reference: reference
       sample: sample
-      knownsites1: knownsites1
+      knownsites: knownsites
       intervallist: splitintervals/intervalfiles
     out: [gvcf]