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genome / analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.
MIT License
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malformed requirements fields #501

Closed chrisamiller closed 5 years ago

chrisamiller commented 5 years ago

There are a bunch of tools that have docker requirements slapped in like this: 

requirements:
    - class: DockerRequirement                                                                                                                                                                                                                                                      dockerPull: "mgibio/bisulfite"
arguments: [
    "--target", {valueFrom: "$(runtime.outdir)/trimmed_read"},
    "--threads", {valueFrom: "$(runtime.cores)"}
]
requirements:
    - class: ResourceRequirement
      ramMin: 16000
      tmpdirMin: 25000
      coresMin: 4

That's bad. Cromwell doesn't pick up on the docker requirements, and submits jobs with no -a or -q parameters, causing the jobs to PEND indefinitely.

They need to be reformatted into a single block like this:

requirements:
    - class: ResourceRequirement
      ramMin: 16000
      tmpdirMin: 25000
      coresMin: 4
    - class: DockerRequirement
      dockerPull: "mgibio/bisulfite"

I'm taking care of the rnaseq-pipeline cwls, but we need a systematic look through to find the rest.

chrisamiller commented 5 years ago

Did some searches and found no other CWLs with this issue. I'm too lazy to trace back the origin, but I suspect it happened in a merge gone awry. Closing!

malachig commented 5 years ago

Interesting. Glad you found the source of that issue!