3 edam: http://edamontology.org/
4 arv: "http://arvados.org/cwl#"
5 s:codeRepository: https://github.com/arvados/arvados-tutorial
6 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
9 label: Convert one chromosome of bam to fastqs
11 ShellCommandRequirement: {}
14 dockerPull: curii/bwa-samtools
18 arv:RuntimeConstraints:
20 outputDirType: keep_output_dir
24 specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
29 #format: edam:format_2572 # BAM
30 label: Alignments in BAM format
31 secondaryFiles: [.bai]
37 label: Chromosome name
41 #format: edam:format_1930 # FASTQ
42 label: One of set of pair-end FASTQs (R1)
47 #format: edam:format_1930 # FASTQ
48 label: One of set of pair-end FASTQs (R2)
51 baseCommand: [samtools, view]
71 valueFrom: "/dev/null"
73 valueFrom: "/dev/null"
75 valueFrom: $(inputs.sample)_1.fastq.gz
77 valueFrom: $(inputs.sample)_2.fastq.gz