cwlVersion: v1.1
class: CommandLineTool
-label: Mark duplicates using GATK (Picard)
+label: Mark duplicates using GATK (Picard)
requirements:
DockerRequirement:
hints:
ResourceRequirement:
ramMin: 20000
- coresMin: 4
+ coresMin: 4
arv:RuntimeConstraints:
outputDirType: keep_output_dir
SoftwareRequirement:
bam:
type: File
format: edam:format_2572 # BAM
- label: Sorted BAM
+ label: Sorted BAM
outputs:
dupbam:
arguments:
- "--java-options"
- - "-Xmx8G"
+ - "-Xmx8G"
- MarkDuplicates
- prefix: "-I"
valueFrom: $(inputs.bam.path)
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl