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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/pangenome-generate/seqwish.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/pangenome-generate/seqwish.cwl')
| -rw-r--r-- | workflows/pangenome-generate/seqwish.cwl | 29 |
1 files changed, 29 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/seqwish.cwl b/workflows/pangenome-generate/seqwish.cwl new file mode 100644 index 0000000..9f8cb15 --- /dev/null +++ b/workflows/pangenome-generate/seqwish.cwl @@ -0,0 +1,29 @@ +cwlVersion: v1.1 +class: CommandLineTool +inputs: + readsFA: File + readsPAF: File + kmerSize: + type: int + default: 16 +outputs: + seqwishGFA: + type: File + outputBinding: + glob: $(inputs.readsPAF.nameroot).gfa +requirements: + InlineJavascriptRequirement: {} +hints: + DockerRequirement: + dockerPull: "quay.io/biocontainers/seqwish:0.4.1--h8b12597_0" + ResourceRequirement: + coresMin: 4 + ramMin: $(7 * 1024) + outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20)) +stdout: $(inputs.readsFA.nameroot).paf +baseCommand: seqwish +arguments: [-t, $(runtime.cores), + -k, $(inputs.kmerSize), + -s, $(inputs.readsFA), + -p, $(inputs.readsPAF), + -g, $(inputs.readsPAF.nameroot).gfa] |