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cwltool SGE support for CWL parallel tasks

I am experimenting with CWL and cwltool. I have successfully written a workflow that can scatter jobs. However, cwltool runs them sequencially, whereas I would like to to use the Sun Grid Engine (SGE) to run jobs in parallel. I looked into Toil to run it but I have found it not capable of running the workflow so far. Here my questions:

  • Does cwltool support integration with SGE?
  • If not, is it planned, and if not, why? Would patches be accepted?
  • Beside Toil, are there working implementation that do interact with SGE?
  • What tools do you use to run cwl workflows with parrallel tasks?

Any other suggestion is welcome.

Thank you

cwl toil sge
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updated by Biostar Biostar • written by Stefano Berri Stefano Berri

1 answer

CWL tool I believe is always planned to just be local runner, and Toil is the only implementation currently with cluster support I believe. Can you post the workflow?

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written by sayerskt • sayerskt

I am getting this message: "CWL Directory inputs not yet supported in Toil"

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written by Stefano Berri Stefano Berri

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