Issues

• switch FastQC process to a multiarch container

  CCBR/CHAMPAGNE#392 · Filter by author kelly-sovacool opened on Oct 19, 2026

• load apptainer instead of singularity

  refactor
  CCBR/CHAMPAGNE#391 · Filter by author kelly-sovacool opened on Oct 19, 2026

• Portability Checklist

  CCBR/CHAMPAGNE#363 · Filter by author github-actions opened on Jul 18, 2026

• Java version error

  bosc-cofest-2026
  CCBR/CHAMPAGNE#358 · Filter by author padmashris opened on Jul 17, 2026

• running via nextflow run CCBR/CHAMPAGNE skips alignment

  bosc-cofest-2026
  CCBR/CHAMPAGNE#357 · Filter by author kelly-sovacool opened on Jul 17, 2026
  1

• make reference genomes more portable

  bosc-cofest-2026
  CCBR/CHAMPAGNE#355 · Filter by author kelly-sovacool opened on Jul 17, 2026
  2

• fastq_screen_conf - support outside of biowulf

  bosc-cofest-2026
  CCBR/CHAMPAGNE#346 · Filter by author kelly-sovacool opened on Jul 17, 2026
  1

• documentation for running outside of biowulf

  bosc-cofest-2026documentation
  CCBR/CHAMPAGNE#344 · Filter by author kelly-sovacool opened on Jul 17, 2026 · 2026-09
  4

  

• strict syntax compliance

  CCBR/CHAMPAGNE#336 · Filter by author kelly-sovacool opened on Jun 10, 2026
  1

• docs: broken links

  automated issuedocumentation
  CCBR/CHAMPAGNE#333 · Filter by author github-actions opened on Jun 4, 2026
  

• use versions topic channel

  CCBR/CHAMPAGNE#322 · Filter by author kelly-sovacool opened on Mar 24, 2026

• fix: skip consensus peak calling if there aren't more than 1 sample per group

  bug
  CCBR/CHAMPAGNE#294 · Filter by author kelly-sovacool opened on Sep 22, 2025
  

• Additional consensus peak strategy: group by antibody across different samples

  enhancement
  CCBR/CHAMPAGNE#293 · Filter by author kelly-sovacool opened on Sep 22, 2025
  

• Create peak counts matrix

  enhancement
  CCBR/CHAMPAGNE#284 · Filter by author kelly-sovacool opened on Aug 14, 2025 · 2025-09
  

• typo in genome config

  CCBR/CHAMPAGNE#280 · Filter by author kelly-sovacool opened on Jul 25, 2025 · 2025-08

• Capture jobby warnings in log file

  CCBR/CHAMPAGNE#274 · Filter by author kelly-sovacool opened on Jul 22, 2025

• Include peak annotations in MultiQC report

  enhancement
  CCBR/CHAMPAGNE#269 · Filter by author kopardev opened on Jul 17, 2025
  

• More species in fastq screen

  enhancement
  CCBR/CHAMPAGNE#268 · Filter by author kopardev opened on Jul 17, 2025
  1

  

• PCA plot of peak callers

  enhancement
  CCBR/CHAMPAGNE#266 · Filter by author kopardev opened on Jul 17, 2025
  

• do not submit slurm job for preview

  bug
  CCBR/CHAMPAGNE#261 · Filter by author kelly-sovacool opened on Jun 23, 2025

• increase stringency of bam filtering

  CCBR/CHAMPAGNE#231 · Filter by author kelly-sovacool opened on Mar 4, 2025

• fix diffbind report

  bug
  CCBR/CHAMPAGNE#228 · Filter by author kelly-sovacool opened on Mar 3, 2025
  

• table in multiqc report showing how reads change at various steps

  enhancement
  CCBR/CHAMPAGNE#221 · Filter by author kelly-sovacool opened on Jan 21, 2025
  5

  

• Only load ccbrpipeliner modules during champagne run (or in slurm script) if it's not already loaded

  bug
  CCBR/CHAMPAGNE#218 · Filter by author kelly-sovacool opened on Jan 16, 2025 · 2025-02
  

• all-vs-all JSD score

  enhancement
  CCBR/CHAMPAGNE#212 · Filter by author kelly-sovacool opened on Nov 20, 2024
  1