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This page:
https://github.com/Sage-Bionetworks/sage-workflows-sandbox/blob/master/docs/cwl_usage/cwl_using-containers.rst
Maybe include background/overview on containers and Docker as well.
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Target date: 2nd week of November, 2023
Yesterday I told @cbielow that I would volunteer to be the release manager for the next release
https://github.com/OpenMS/OpenMS/wiki/Preparation-of-a-new…
mr-c updated
4 months ago
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While [converting a `cwltool --provenance` RO to a Workflow Run RO-Crate](https://github.com/ResearchObject/workflow-run-crate/pull/5), I'm faced with the problem of referring to individual workflow s…
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- [x] Fix the links in the source column by removing the "api." substring so anyone can be directed to the source file without any error
- [x] Do some data analysis. Check how many cwl files had issue…
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See https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update for full description of each task (requires gitlab login)
- assembly accession number: GCF_037126465.1
…
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When using `toil-cwl-runner` it seems like it always uses `deep_listing` when files or directories are mounted for running within Docker or Singularity.
If I try to add [LoadListingRequirement](https…
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# OGS remapping
- [ ] request whole-genome alignment
- [ ] Set up data directories and get data
- [ ] run remap-gff3
# manual annotations remapping
- [ ] request whole-genome alignment
- […
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One of the more complex issue about getting workflow engines deployed is that many of them have to read the contents of at least one file to proceed. For CWL, there is the potential of a `cwl.output.j…
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# OGS remapping
- [ ] request whole-genome alignment
- [ ] Set up data directories and get data
- [ ] run remap-gff3
# Change old content
- [ ] back up and deprecate old Apollo2
- [ ] back u…
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# OGS remapping
- [ ] request whole-genome alignment
- [ ] Set up data directories and get data
- [ ] run remap-gff3
# Change old content
- [ ] back up and deprecate old Apollo2
- [ ] back …