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:
  • Fraction in Peaks (FRiP) (#89)
  • Jaccard index (#92)
  • Histogram of peak widths (#92)
• 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 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)

Full Changelog: v0.1.0...v0.2.0