+++ /dev/null
-cwlVersion: v1.1
-class: CommandLineTool
-label: Realigning fastqs and converting output to bam
-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
-
-requirements:
- DockerRequirement:
- dockerPull: curii/bwa-samtools-picard
- ShellCommandRequirement: {}
- ResourceRequirement:
- ramMin: 26000
- coresMin: 16
-
-hints:
- arv:RuntimeConstraints:
- outputDirType: keep_output_dir
-
-inputs:
- reference:
- type: File
- secondaryFiles:
- - .amb
- - .ann
- - .bwt
- - .pac
- - .sa
- - .fai
- - ^.dict
- fastq1: File
- fastq2: File
- sample: string
-
-stdout: $(inputs.sample).bam
-
-outputs:
- bam:
- type: File
- outputBinding:
- glob: "*bam"
-
-arguments:
- - /bwa-0.7.17/bwa
- - mem
- - -M
- - -t
- - $(runtime.cores)
- - $(inputs.reference)
- - -R
- - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
- - -c
- - 250
- - $(inputs.fastq1)
- - $(inputs.fastq2)
- - shellQuote: false
- valueFrom: '|'
- - samtools
- - view
- - -@
- - $(runtime.cores)
- - -b
- - -S
- - shellQuote: false
- valueFrom: '-'