3 label: Align FASTQs with BWA
7 dockerPull: curii/bwa-samtools-picard
8 ShellCommandRequirement: {}
14 arv:RuntimeConstraints:
16 outputDirType: keep_output_dir
20 specs: [ "https://identifiers.org/rrid/RRID:SCR_010910" ]
23 specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
29 format: edam:format_1929 # FASTA
30 label: Reference genome
41 format: edam:format_1930 # FASTQ
42 label: One of set of pair-end FASTQs (R1)
45 format: edam:format_1930 # FASTQ
46 label: One of set of pair-end FASTQs (R2)
51 stdout: $(inputs.sample).bam
56 format: edam:format_2572 # BAM
57 label: Alignments in BAM format
69 - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
85 s:codeRepository: https://github.com/arvados/arvados-tutorial
86 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
89 s: https://schema.org/
90 edam: http://edamontology.org/
91 arv: "http://arvados.org/cwl#"
92 cwltool: "http://commonwl.org/cwltool#"
95 - https://schema.org/version/latest/schema.rdf
96 - http://edamontology.org/EDAM_1.18.owl