Releases: CCBR/CHAMPAGNE
Releases · CCBR/CHAMPAGNE
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 withpip
. (#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
.
- However, any dependencies not in the Python Standard Library must be installed for this to work. See the dependencies list in
- 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
- These equivalent commands now work:
- 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)
CHAMPAGNE 0.3.0
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)
- Support multiple replicates per sample and call consensus peaks on replicates. (#129)
- Optionally normalize p-values with the 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 rundiffbind
.
- Print the recommended citation in bibtex format with
champagne --citation
. (#153)- CHAMPAGNE is also now archived in Zenodo with DOI
10.5281/zenodo.10516078
.
- CHAMPAGNE is also now archived in Zenodo with DOI
- The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#170)
Bug fixes
- Fix deepTools plots (#144):
- Per sample fingerprint plots instead of per replicate.
- Input normalized profile plots.
- Protein-coding-only versions of plots.
- Ensure sample IDs are sorted. (#150)
- 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)
- Fix broken bold styling in documentation website. (#53)
CHAMPAGNE 0.2.2
- Fix permissions issues in the CLI. (#167)
CHAMPAGNE 0.2.1
- Fixed a bug in QC stats that mixed up the statistics for different samples. (#125)
- Fixed 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).
Full Changelog: v0.2.0...v0.2.1
CHAMPAGNE 0.2.0
New features
- Implemented peak calling with sicer2, macs2, and gem. (#52)
- Added parameter options to skip QC, input normalization, and/or peak calling steps. (#72)
- Calculate and plot QC metrics for called peaks:
- Added support for paired-end reads. (#105)
- Added an option to use a custom reference from a genome fasta, gtf, and blacklist file. (#105)
- Champagne CLI: (#112)
- New
--mode
option forchampagne run
to execute the workflow locally ('local') or submit it as a slurm job ('slurm'). - Option to override the path to the champagne
main.nf
file or specify the github repo (CCBR/CHAMPAGNE
) instead.# use the default path champagne run ... # override the path champagne run path/to/champagne/main.nf # use a revision from github instead champagne run CCBR/CHAMPAGNE -r v0.1.0
- New
Bug fixes
- CLI:
- Containers:
- Containers are now specified in process definitions instead of
withName
/withLabel
for better control. (#69)- Shared containers are specified as parameters in the config file
conf/containers.config
.
- Shared containers are specified as parameters in the config file
- No longer use
--mount type=bind
or--volume
for making directories available to processes in containers. Instead, use Nextflow'sChannel.fromPath
constructor withtype: 'dir'
. (#71)
- Containers are now specified in process definitions instead of
API-breaking changes
- An error is thrown when a required input file doesn't exist. (#71)
- Previously, the workflow quietly didn't run the process(es) that required the missing file.
- Renamed
champagne config
tochampagne init
to avoid clashing withnextflow config
. (#112)
Full Changelog: v0.1.0...v0.2.0
CHAMPAGNE v0.1.0
This release implements nearly all QC steps from the original CCBR pipeliner chip-seq workflow.
Quality control steps implemented for single-end reads
- Trim raw reads, FastQC on raw and trimmed reads, and FastQ Screen on trimmed reads.
- Exclude reads that align to blacklist regions, align remaining reads to the reference genome, and deduplicate.
- Preseq on aligned reads.
- Phantompeakqualtools on aligned and deduplicated reads.
- Process reads with deepTools: bam coverage to generate bigwigs for each sample, summarize all bigwigs, and compute matrices relative to TSSs and scaled to metagene regions.
- Generate plots with deepTools: PCA, profile, heatmap, spearman correlation, and fingerprint plots.
- Summarize all quality control steps in a MultiQC report.
- Input-normalize ChIP fragments for the next stage of the pipeline.