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| author | Pjotr Prins | 2020-12-24 09:15:39 +0000 |
|---|---|---|
| committer | GitHub | 2020-12-24 09:15:39 +0000 |
| commit | df0421757e464f07b5e96b5444f1926784e7400f (patch) | |
| tree | f9a9a262bb2d95a89a6ec1c96b98a2b166fb92b5 /workflows/pangenome-generate/abpoa.cwl | |
| parent | 00ba74b163f723bb7283624171f0c7c203dc99e5 (diff) | |
| parent | bfd830f9d777c456409958030142155043ec1c68 (diff) | |
| download | bh20-seq-resource-df0421757e464f07b5e96b5444f1926784e7400f.tar.gz bh20-seq-resource-df0421757e464f07b5e96b5444f1926784e7400f.tar.lz bh20-seq-resource-df0421757e464f07b5e96b5444f1926784e7400f.zip | |
Merge pull request #117 from arvados/pangenome_workflow_abpoa
Pangenome workflow with abPOA
Diffstat (limited to 'workflows/pangenome-generate/abpoa.cwl')
| -rw-r--r-- | workflows/pangenome-generate/abpoa.cwl | 26 |
1 files changed, 26 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/abpoa.cwl b/workflows/pangenome-generate/abpoa.cwl new file mode 100644 index 0000000..fa9f157 --- /dev/null +++ b/workflows/pangenome-generate/abpoa.cwl @@ -0,0 +1,26 @@ +cwlVersion: v1.1 +class: CommandLineTool +inputs: + readsFA: File + script: + type: File + default: {class: File, location: relabel-seqs.py} +outputs: + abpoaGFA: + type: stdout +requirements: + InlineJavascriptRequirement: {} +hints: + DockerRequirement: + dockerPull: "quay.io/biocontainers/abpoa:1.0.5--hed695b0_0" + ResourceRequirement: + coresMin: 1 + ramMin: $(15 * 1024) + outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20)) +baseCommand: abpoa +stdout: $(inputs.readsFA.nameroot).O0.gfa +arguments: [ + $(inputs.readsFA), + -r 3, + -O, '0' +] |