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| author | AndreaGuarracino | 2020-07-23 22:28:37 +0200 |
|---|---|---|
| committer | AndreaGuarracino | 2020-07-27 12:15:05 +0200 |
| commit | 088d0a7fa47d4dff5a38f42fe4d12b9841bb033e (patch) | |
| tree | 3691ea7c09803bb974714b4418c799f743dab03b /workflows/pangenome-generate | |
| parent | 8e052cb7355eed7ce4d7075b23c9b0439285f84e (diff) | |
| download | bh20-seq-resource-088d0a7fa47d4dff5a38f42fe4d12b9841bb033e.tar.gz bh20-seq-resource-088d0a7fa47d4dff5a38f42fe4d12b9841bb033e.tar.lz bh20-seq-resource-088d0a7fa47d4dff5a38f42fe4d12b9841bb033e.zip | |
new workflow for odgi building from spoa gfa
Diffstat (limited to 'workflows/pangenome-generate')
| -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 + ] |