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| author | AndreaGuarracino | 2020-07-27 17:04:00 +0200 |
|---|---|---|
| committer | AndreaGuarracino | 2020-07-27 17:04:00 +0200 |
| commit | e31d89f6b4c0d2a99eb6df90b85b4e51cb584817 (patch) | |
| tree | 8407f5b9a0a2a8df3b9f1dbdcfe94b2f76525af9 | |
| parent | 088d0a7fa47d4dff5a38f42fe4d12b9841bb033e (diff) | |
| download | bh20-seq-resource-e31d89f6b4c0d2a99eb6df90b85b4e51cb584817.tar.gz bh20-seq-resource-e31d89f6b4c0d2a99eb6df90b85b4e51cb584817.tar.lz bh20-seq-resource-e31d89f6b4c0d2a99eb6df90b85b4e51cb584817.zip | |
added spoa workflow in a low memory consumption mode
| -rw-r--r-- | workflows/pangenome-generate/spoa.cwl | 27 |
1 files changed, 27 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/spoa.cwl b/workflows/pangenome-generate/spoa.cwl new file mode 100644 index 0000000..1e390d8 --- /dev/null +++ b/workflows/pangenome-generate/spoa.cwl @@ -0,0 +1,27 @@ +cwlVersion: v1.1 +class: CommandLineTool +inputs: + readsFA: File +stdout: $(inputs.readsFA.nameroot).g6.gfa +script: + type: File + default: {class: File, location: relabel-seqs.py} +outputs: + spoaGFA: + type: stdout +requirements: + InlineJavascriptRequirement: {} + ShellCommandRequirement: {} +hints: + DockerRequirement: + dockerPull: "quay.io/biocontainers/spoa:3.0.2--hc9558a2_0" + ResourceRequirement: + coresMin: 1 + ramMin: $(15 * 1024) + outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20)) +baseCommand: spoa +arguments: [ + $(inputs.readsFA), + -G, + -g, '-6' +] |