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| author | Peter Amstutz | 2020-08-19 15:19:07 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-08-19 16:31:38 -0400 |
| commit | b3d2ccf951903ac0b7d717357fb1cccca26fbd15 (patch) | |
| tree | 92adcacbd208546bf3f063e6c25765e660972244 /workflows/pangenome-generate/collect-seqs.cwl | |
| parent | 592c921a3223c03d8a22f7a852641ac5d753fb31 (diff) | |
| download | bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.tar.gz bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.tar.lz bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.zip | |
Consolidate steps to scale graph generation workflow
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/pangenome-generate/collect-seqs.cwl')
| -rw-r--r-- | workflows/pangenome-generate/collect-seqs.cwl | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/collect-seqs.cwl b/workflows/pangenome-generate/collect-seqs.cwl new file mode 100644 index 0000000..3511df1 --- /dev/null +++ b/workflows/pangenome-generate/collect-seqs.cwl @@ -0,0 +1,42 @@ +cwlVersion: v1.1 +class: CommandLineTool +$namespaces: + arv: "http://arvados.org/cwl#" + cwltool: "http://commonwl.org/cwltool#" +requirements: + arv:APIRequirement: {} + arv:RuntimeConstraints: + outputDirType: keep_output_dir + DockerRequirement: + dockerPull: arvados/jobs:2.0.3 + WorkReuse: + enableReuse: false + ResourceRequirement: + coresMin: 1 + ramMin: 1024 +baseCommand: python3 +inputs: + script: + type: File + default: + class: File + location: collect-seqs.py + inputBinding: {position: 1} + src_project: + type: string + inputBinding: {position: 2} + schema: + type: File + inputBinding: {position: 3} + exclude: + type: File? + inputBinding: {position: 4} +outputs: + relabeledSeqs: + type: File + outputBinding: + glob: relabeledSeqs.fasta + mergedMetadata: + type: File + outputBinding: + glob: mergedMetadata.ttl |