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chore: update changelog
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kelly-sovacool committed Jul 12, 2024
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## CHAMPAGNE development version

### 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:
```sh
nextflow run CCBR/CHAMPAGNE
champagne run --main CCBR/CHAMPAGNE
```
- Allow multiple samples to use the same input. (#176, @kelly-sovacool)
- Allow additional columns in the sample sheet beyond the minimum required header. (#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)

### Misc

- Change the peak widths histogram type from overlay to stack. (#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)
- In biowulf config profile, switch variable $SLURM_JOBID to $SLURM_JOB_ID. (@kelly-sovacool)
- Documentation improvements. (#192, @slsevilla)

## CHAMPAGNE 0.3.0

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