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Removing initial work dir requirement when not needed
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
gatk-baserecalibrator-with-interval.cwl
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"