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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/odgi-build-from-xpoa-gfa.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/odgi-build-from-xpoa-gfa.cwl')
| -rw-r--r-- | workflows/pangenome-generate/odgi-build-from-xpoa-gfa.cwl | 29 |
1 files changed, 29 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/odgi-build-from-xpoa-gfa.cwl b/workflows/pangenome-generate/odgi-build-from-xpoa-gfa.cwl new file mode 100644 index 0000000..eee4031 --- /dev/null +++ b/workflows/pangenome-generate/odgi-build-from-xpoa-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: {} +hints: + DockerRequirement: + dockerPull: "odgi-bash-binutils:latest" + ResourceRequirement: + coresMin: 4 + ramMin: $(15 * 1024) + outdirMin: $(Math.ceil((inputs.inputGFA.size/(1024*1024*1024)+1) * 2)) + InitialWorkDirRequirement: + # Will fail if input file is not writable (odgi bug) + listing: + - entry: $(inputs.inputGFA) + writable: true +arguments: + - "sh" + - "-c" + - >- + odgi build -g '$(inputs.inputGFA.path)' -o - | odgi unchop -i - -o - | + odgi sort -i - -p s -o $(inputs.inputGFA.nameroot).unchop.sorted.odgi |