Client Updates

[tmsincomb]

• 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