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CHAMPAGNE development version

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)

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)
  • 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

  • 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

  • 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

  • Implement peak calling with sicer2, macs2, and gem. (#52)
  • Add parameter options to skip QC, input normalization, and/or peak calling steps. (#72)
  • Calculate and plot QC metrics for called peaks:
    • Fraction in Peaks (FRiP) (#89)
    • Jaccard index (#92)
    • Histogram of peak widths (#92)
  • Add support for paired-end reads. (#105)
  • Add an option to use a custom reference from a genome fasta, gtf, and blacklist file. (#105)
  • Champagne CLI: (#112)
    • New --mode option for champagne 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

Bug fixes

  • CLI:
    • Error when biowulf-specific environment variables are not defined. (#54)
    • The host is now correctly detected as biowulf via scontrol. (#75)
  • 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.
    • No longer use --mount type=bind or --volume for making directories available to processes in containers. Instead, use Nextflow's Channel.fromPath constructor with type: 'dir'. (#71)

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 to champagne init to avoid clashing with nextflow config. (#112)

CHAMPAGNE 0.1.0

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.