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| author | Peter Amstutz | 2020-08-05 16:06:11 -0400 |
|---|---|---|
| committer | GitHub | 2020-08-05 16:06:11 -0400 |
| commit | fdb1b012fc04ee07f401541e181e28fe442c9454 (patch) | |
| tree | 8486db1087692dffcea9d93814e436d9cf150b47 /workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl | |
| parent | 86f31ef60f65a820bf9ac25c3fc01c88f2a9ebfe (diff) | |
| parent | 2d20bf90497588a297ca98a78ee0fbbcadf95569 (diff) | |
| download | bh20-seq-resource-fdb1b012fc04ee07f401541e181e28fe442c9454.tar.gz bh20-seq-resource-fdb1b012fc04ee07f401541e181e28fe442c9454.tar.lz bh20-seq-resource-fdb1b012fc04ee07f401541e181e28fe442c9454.zip | |
Merge pull request #99 from AndreaGuarracino/patch-2
several fixes in the website, added links to video talk and poster, new pangenome generation workflow
Diffstat (limited to 'workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl')
| -rw-r--r-- | workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl | 29 |
1 files changed, 29 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl b/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl new file mode 100644 index 0000000..2459ce7 --- /dev/null +++ b/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl @@ -0,0 +1,29 @@ +cwlVersion: v1.1 +class: CommandLineTool +inputs: + inputGFA: File +outputs: + odgiGraph: + type: File + outputBinding: + glob: $(inputs.inputGFA.nameroot).unchop.sorted.odgi +requirements: + InlineJavascriptRequirement: {} + ShellCommandRequirement: {} +hints: + DockerRequirement: + dockerPull: "quay.io/biocontainers/odgi:v0.3--py37h8b12597_0" + ResourceRequirement: + coresMin: 4 + ramMin: $(7 * 1024) + outdirMin: $(Math.ceil((inputs.inputGFA.size/(1024*1024*1024)+1) * 2)) + InitialWorkDirRequirement: + listing: + - entry: $(inputs.inputGFA) + writable: true +arguments: [odgi, build, -g, $(inputs.inputGFA), -o, -, + {shellQuote: false, valueFrom: "|"}, + odgi, unchop, -i, -, -o, -, + {shellQuote: false, valueFrom: "|"}, + odgi, sort, -i, -, -p, s, -o, $(inputs.inputGFA.nameroot).unchop.sorted.odgi + ] |