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| author | Peter Amstutz | 2020-04-20 12:55:18 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-20 12:55:18 -0400 |
| commit | d781e42c9adac07253cb928ae66e9b7314710267 (patch) | |
| tree | 4718165cbc069169eaff98080c61c5f07763ffc1 /workflows/fastq2fasta/bwa-index.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-index.cwl')
| -rw-r--r-- | workflows/fastq2fasta/bwa-index.cwl | 32 |
1 files changed, 32 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/bwa-index.cwl b/workflows/fastq2fasta/bwa-index.cwl new file mode 100644 index 0000000..775ba8d --- /dev/null +++ b/workflows/fastq2fasta/bwa-index.cwl @@ -0,0 +1,32 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.1 +class: CommandLineTool +doc: string +requirements: + DockerRequirement: + dockerPull: quay.io/biocontainers/bwa:0.7.17--h84994c4_5 + InitialWorkDirRequirement: + listing: + - $(inputs.input_fasta) +baseCommand: [bwa, index] +inputs: + input_fasta: + type: File + label: "input fasta file" + inputBinding: + position: 1 +outputs: + indexed_fasta: + type: File + outputBinding: + glob: $(inputs.input_fasta.basename) + secondaryFiles: + - .amb + - .ann + - .bwt + - .pac + - .sa + stdout: stdout + stderr: stderr +stdout: bwa-index-stdout.log +stderr: bwa-index-stderr.log |