Removing initial work dir requirement when not needed

[arvados-tutorial.git] / WGS-processing / cwl / helper / gatk-applyBSQR-with-interval.cwl

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
-  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"