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| author | AndreaGuarracino | 2020-11-21 23:06:05 +0100 |
|---|---|---|
| committer | AndreaGuarracino | 2020-11-21 23:06:05 +0100 |
| commit | 1e9a735e84a8e89099b1de2ec66c56669caf6cc8 (patch) | |
| tree | 0beefb8e9f7a6321a5c8382b1be7b5b809c87d5e /workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl | |
| parent | 862ae0235e3d1b105fa342cedf4aa59ae73d90c4 (diff) | |
| download | bh20-seq-resource-1e9a735e84a8e89099b1de2ec66c56669caf6cc8.tar.gz bh20-seq-resource-1e9a735e84a8e89099b1de2ec66c56669caf6cc8.tar.lz bh20-seq-resource-1e9a735e84a8e89099b1de2ec66c56669caf6cc8.zip | |
added abPOA workflow; typos
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, 0 insertions, 29 deletions
diff --git a/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl b/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl deleted file mode 100644 index eee4031..0000000 --- a/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl +++ /dev/null @@ -1,29 +0,0 @@ -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 |