diff options
Diffstat (limited to 'workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl')
| -rw-r--r-- | workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl | 16 |
1 files changed, 8 insertions, 8 deletions
diff --git a/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl b/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl index 2459ce7..1eadc88 100644 --- a/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl +++ b/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl @@ -9,21 +9,21 @@ outputs: glob: $(inputs.inputGFA.nameroot).unchop.sorted.odgi requirements: InlineJavascriptRequirement: {} - ShellCommandRequirement: {} hints: DockerRequirement: - dockerPull: "quay.io/biocontainers/odgi:v0.3--py37h8b12597_0" + dockerPull: "odgi-bash-binutils:latest" ResourceRequirement: coresMin: 4 ramMin: $(7 * 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: [odgi, build, -g, $(inputs.inputGFA), -o, -, - {shellQuote: false, valueFrom: "|"}, - odgi, unchop, -i, -, -o, -, - {shellQuote: false, valueFrom: "|"}, - odgi, sort, -i, -, -p, s, -o, $(inputs.inputGFA.nameroot).unchop.sorted.odgi - ] +arguments: + - "sh" + - "-c" + - >- + odgi build -g '$(inputs.inputGFA.path)' -o - | odgi unchop -i - -o - | + odgi sort -i - -p s -o $(inputs.inputGFA.nameroot).unchop.sorted.odgi |