Skip to content

Commit

Permalink
chore: prep changelog for release
Browse files Browse the repository at this point in the history
  • Loading branch information
kelly-sovacool committed Jan 18, 2024
1 parent 0e084b0 commit 38c5b08
Showing 1 changed file with 3 additions and 6 deletions.
9 changes: 3 additions & 6 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,17 +1,18 @@
## development version
## CHAMPAGNE development version

### New features

- Find motifs in the genome with Homer. (#142)
- Run motif enrichment analysis with MEME. (#142)
- Annotate peaks with chipseeker. (#142,#147,#157)
- Add preseq complexity curve and fastq screen to multiqc report. (#147)
- Print the recommended citation in bibtex format with `champagne --citation`. (#153)
- Support multiple replicates per sample and call consensus peaks on replicates. (#129)
- Optionally normalize p-values with the [CCBR/consensus_peaks](https://github.com/CCBR/nf-modules/tree/60d50f4c45a50378cad70b49013f51750617caaa/subworkflows/CCBR/consensus_peaks) subworkflow.
- Implement differential peak calling. (#158)
- Optionally specify contrasts via a YAML file. If no file is specified, differential analysis is not performed.
- If any sample has only one replicate, run `MAnorm`, otherwise run `diffbind`.
- Print the recommended citation in bibtex format with `champagne --citation`. (#153)
- CHAMPAGNE is also now archived in Zenodo with DOI `10.5281/zenodo.10516078`.
- The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#170)

### Bug fixes
Expand All @@ -24,20 +25,17 @@
- Fix a bug where the wrong SICER output file was used for downstream analyses. (#155)
- Fix CLI profile on machines other than biowulf & FRCE. (#168)


## CHAMPAGNE 0.2.2

- Fix permissions issues in the CLI. (#167)


## CHAMPAGNE 0.2.1

- Fix a bug in QC stats that mixed up the statistics for different samples. (#125)
- Fix a bug in the CLI that added the `-profile` to the nextflow command even if it wasn't needed (#125).
- Report read counts between blacklist & filtering steps in the QC table. (#125)
- Run spooker on workflow completion (#126).


## CHAMPAGNE 0.2.0

### New features
Expand Down Expand Up @@ -78,7 +76,6 @@
- Previously, the workflow quietly didn't run the process(es) that required the missing file.
- Renamed `champagne config` to `champagne init` to avoid clashing with `nextflow config`. (#112)
## CHAMPAGNE 0.1.0
### Quality control steps implemented for single-end reads
Expand Down

0 comments on commit 38c5b08

Please sign in to comment.