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author | Peter Amstutz | 2020-04-20 12:55:18 -0400 |
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committer | Peter Amstutz | 2020-04-20 12:55:18 -0400 |
commit | d781e42c9adac07253cb928ae66e9b7314710267 (patch) | |
tree | 4718165cbc069169eaff98080c61c5f07763ffc1 /workflows/fastq2fasta/bwa-mem.cwl | |
parent | 1219eaf496c899f3043b90e30eb956f0f363bfb3 (diff) | |
download | bh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.tar.gz bh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.tar.lz bh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.zip |
Move workflows into main repo
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/fastq2fasta/bwa-mem.cwl')
-rw-r--r-- | workflows/fastq2fasta/bwa-mem.cwl | 59 |
1 files changed, 59 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/bwa-mem.cwl b/workflows/fastq2fasta/bwa-mem.cwl new file mode 100644 index 0000000..195411c --- /dev/null +++ b/workflows/fastq2fasta/bwa-mem.cwl @@ -0,0 +1,59 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.1 +class: CommandLineTool +doc: string +requirements: + DockerRequirement: + dockerPull: quay.io/biocontainers/bwa:0.7.17--h84994c4_5 + +baseCommand: [bwa, mem] + +inputs: + threads: + type: int + label: "number of threads" + default: 4 + inputBinding: + prefix: -t + output_sam: + type: string + label: "sam file to output results to" + default: "out.sam" + inputBinding: + prefix: -o + group_header_line: + type: string? + label: "read group header line such as '@RG\tID:foo\tSM:bar'" + inputBinding: + prefix: -R + index_base: + type: File + label: "fasta file for index basename" + inputBinding: + position: 1 + secondaryFiles: + - .amb + - .ann + - .bwt + - .pac + - .sa + fastq_forward: + type: File + label: "input fastq file to map (single-end or forward for pair-end)" + inputBinding: + position: 2 + fastq_reverse: + type: File? + label: "input fastq file to map (reverse for pair-end)" + inputBinding: + position: 3 + +outputs: + output: + type: File + outputBinding: + glob: "$(inputs.output_sam)" + stdout: stdout + stderr: stderr +stdout: bwa-mem-stdout.log +stderr: bwa-mem-stderr.log |