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Removing initial work dir requirement when not needed
authorSarah Wait Zaranek <swz@curii.com>
Fri, 3 Jul 2020 13:31:35 +0000 (13:31 +0000)
committerSarah Wait Zaranek <swz@curii.com>
Fri, 3 Jul 2020 13:31:35 +0000 (13:31 +0000)
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl patch | blob | history
WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl patch | blob | history

diff --git a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
index d8f6afd07ecc684d30a4739f9f5cabc39a56eb47..52413a6ea4958dd60c2d433ee1af308decb9b0b8 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
@@ -5,9 +5,6 @@ label: Apply base quality score recalibration
 requirements:
   DockerRequirement:
     dockerPull: broadinstitute/gatk:4.1.7.0
 requirements:
   DockerRequirement:
     dockerPull: broadinstitute/gatk:4.1.7.0
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.bam)
 
 hints:
   arv:RuntimeConstraints:
 
 hints:
   arv:RuntimeConstraints:
@@ -70,7 +67,7 @@ arguments:
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"
-    valueFrom: $(inputs.bam.basename)
+    valueFrom: $(inputs.bam)
   - prefix: "--bqsr-recal-file"
     valueFrom: $(inputs.recaltable)
   - prefix: "-L"
   - prefix: "--bqsr-recal-file"
     valueFrom: $(inputs.recaltable)
   - prefix: "-L"
diff --git a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
index 80859e64a6eb752e0b67498cc98185adf9421e55..7ae08377f143563bd425ed4314d4b7af8d5a8d39 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
@@ -5,9 +5,6 @@ label: Generate recalibration table for BQSR
 requirements:
   DockerRequirement:
     dockerPull: broadinstitute/gatk:4.1.7.0
 requirements:
   DockerRequirement:
     dockerPull: broadinstitute/gatk:4.1.7.0
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.bam)
 
 hints:
   arv:RuntimeConstraints:
 
 hints:
   arv:RuntimeConstraints:
@@ -70,7 +67,7 @@ arguments:
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"
-    valueFrom: $(inputs.bam.basename)
+    valueFrom: $(inputs.bam)
   - prefix: "--known-sites"
     valueFrom: $(inputs.knownsites)
   - prefix: "-L"
   - prefix: "--known-sites"
     valueFrom: $(inputs.knownsites)
   - prefix: "-L"