dockerPull: curii/bwa-samtools-picard
ShellCommandRequirement: {}
ResourceRequirement:
- ramMin: 26000
+ ramMin: 20000
coresMin: 16
hints:
arv:RuntimeConstraints:
outputDirType: keep_output_dir
+ keep_cache: 9216
inputs:
reference:
- samtools
- sort
- -@
- - $(runtime.cores)
+ - '16'
- -m
- - '2G'
+ - '500M'
- -l
- '6'
- -o
--- /dev/null
+cwlVersion: v1.1
+class: CommandLineTool
+label: Generating recalibration table for BQSR
+
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+ DockerRequirement:
+ dockerPull: broadinstitute/gatk:4.1.7.0
+ InitialWorkDirRequirement:
+ listing:
+ - $(inputs.bam)
+
+hints:
+ arv:RuntimeConstraints:
+ outputDirType: keep_output_dir
+ keep_cache: 1024
+ ResourceRequirement:
+ ramMin: 5000
+ coresMin: 2
+
+inputs:
+ bam:
+ type: File
+ reference:
+ type: File
+ secondaryFiles:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+ - .fai
+ - ^.dict
+ sample: string
+ knownsites1:
+ type: File
+ secondaryFiles:
+ - .tbi
+
+outputs:
+ recaltable:
+ type: File
+ outputBinding:
+ glob: "*.table"
+
+baseCommand: /gatk/gatk
+
+arguments:
+ - "--java-options"
+ - "-Xmx4G"
+ - BaseRecalibrator
+ - prefix: "-R"
+ valueFrom: $(inputs.reference)
+ - prefix: "-I"
+ valueFrom: $(inputs.bam.basename)
+ - prefix: "--known-sites"
+ valueFrom: $(inputs.knownsites1)
+ - prefix: "-O"
+ valueFrom: $(inputs.sample)_recal_data.table