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Client Updates #19

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Client Updates #19

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@tmsincomb tmsincomb commented Dec 6, 2022

  • readme.rst -> readme.md
    Sphinx not used so complicating it for rst is not useful.
  • wrapping cwltool for client usage
salmon-rnaseq --assay ASSAY --fastq_dir FASTQ_DIR --threads THREADS
  • pytest for client
    Testing for client only to make sure IO is working
  • docker-compose.yaml
    Easier for devs to update code live without rebuilding an image.
# launch container
docker-compose up
  • github workflows for pytest & pre-commit

    • not practical if docker image 50GBs+ needed to be loaded on a workflow job
  • verify salmon bug

    • pipeline failed due to needing 28gbs as requirement for docker instance
  • tests that fit in github

Recommended Updates

  • pytest for .py files in bin/*
  • docstrings and comments.
  • Accept unpaired fastq files as input option
salmon-rnaseq --assay ASSAY --fastq_single FASTQ_FILE 

@tmsincomb tmsincomb marked this pull request as draft December 6, 2022 18:33
@tmsincomb tmsincomb marked this pull request as ready for review February 14, 2023 20:06
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