diff options
| author | Peter Amstutz | 2020-04-20 12:55:18 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-20 12:55:18 -0400 |
| commit | d781e42c9adac07253cb928ae66e9b7314710267 (patch) | |
| tree | 4718165cbc069169eaff98080c61c5f07763ffc1 /workflows/pangenome-generate/odgi-build.cwl | |
| parent | 1219eaf496c899f3043b90e30eb956f0f363bfb3 (diff) | |
| download | bh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.tar.gz bh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.tar.lz bh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.zip | |
Move workflows into main repo
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/pangenome-generate/odgi-build.cwl')
| -rw-r--r-- | workflows/pangenome-generate/odgi-build.cwl | 26 |
1 files changed, 26 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/odgi-build.cwl b/workflows/pangenome-generate/odgi-build.cwl new file mode 100644 index 0000000..0bd6a20 --- /dev/null +++ b/workflows/pangenome-generate/odgi-build.cwl @@ -0,0 +1,26 @@ +cwlVersion: v1.1 +class: CommandLineTool +inputs: + inputGFA: File +outputs: + odgiGraph: + type: File + outputBinding: + glob: $(inputs.inputGFA.nameroot).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), -s, -o, -, + {shellQuote: false, valueFrom: "|"}, + odgi, sort, -i, -, -p, s, -o, $(inputs.inputGFA.nameroot).odgi] |