CHAMPAGNE 0.4.0

New features

• Create a script (bin/champagne) to provide an interface to the champagne CLI that works out-of-the-box without the need to install the python package with pip. (#180, @kelly-sovacool)
  • However, any dependencies not in the Python Standard Library must be installed for this to work. See the dependencies list in pyproject.toml.
• Allow additional columns in the sample sheet beyond the minimum required header. (#176, @kelly-sovacool)
• Add a workflow entry point to download fastq files from SRA. (#176, @kelly-sovacool)
• Add test_human profile with chipseq data from ENCODE. (#176, @kelly-sovacool)

Bug fixes

• Fix configuration files for compatibility with using the GitHub repo as the source. (#173, @kelly-sovacool)
  • These equivalent commands now work:

    nextflow run CCBR/CHAMPAGNE
    champagne run --main CCBR/CHAMPAGNE

• Allow multiple samples to use the same input. (#176, @kelly-sovacool)
• In the biowulf config profile, switch variable $SLURM_JOBID to $SLURM_JOB_ID. (@kelly-sovacool)
• Increase resource allocations for chipseeker and deeptools. (#192, @slsevilla)
• Check the validity of the contrastsheet earlier on in the workflow. (#192, @slsevilla; #200, @kelly-sovacool)
• Fix bug where manorm was using R1 twice instead of R1 and R2. (#206, @kelly-sovacool)

Misc

• Change the peak widths histogram type from overlay to stack. (#176, @kelly-sovacool)
• Documentation improvements. (#192, @slsevilla)