From: Sarah Wait Zaranek <swz@curii.com>
Date: Fri, 3 Jul 2020 13:31:35 +0000 (+0000)
Subject: Removing initial work dir requirement when not needed
X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/48f2b200216c57788577d45e080ab6bae212f90b

Removing initial work dir requirement when not needed
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
---

diff --git a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
index d8f6afd..52413a6 100644
--- 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
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.bam)
 
 hints:
   arv:RuntimeConstraints:
@@ -70,7 +67,7 @@ arguments:
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"
-    valueFrom: $(inputs.bam.basename)
+    valueFrom: $(inputs.bam)
   - 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 80859e6..7ae0837 100644
--- 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
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.bam)
 
 hints:
   arv:RuntimeConstraints:
@@ -70,7 +67,7 @@ arguments:
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"
-    valueFrom: $(inputs.bam.basename)
+    valueFrom: $(inputs.bam)
   - prefix: "--known-sites"
     valueFrom: $(inputs.knownsites)
   - prefix: "-L"