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Published June 12, 2023 | Version 2.4.0
Software Open

nf-core/methylseq: [2.4.0] Gillespie Gaia

Creators

  • 1. @seqeralabs
  • 2. @imbforge
  • 3. Van Andel Institute
  • 4. @ScilifelabDataCentre
  • 5. Boehringer Ingelheim
  • 6. QBiC @qbicsoftware
  • 7. National Genomics Infrastructure
  • 8. Seqera Labs
  • 9. @seqeralabs | Stockholm
  • 10. Altos Labs, Cambridge Institute of Science
  • 11. INRAE
  • 12. CLEVELAND CLINIC
  • 13. AIRAmed

Description

Pipeline Updates

  • Updated template to nf-core/tools v2.8
  • Add --bamqc_regions_file parameter for targeted methylation sequencing data #302
  • ✨ Add NF-TEST tests and snapshots for the pipeline test profile #310
Bug fixes & refactoring
  • 🛠️ update index file channels to explicit value channels #310
  • 🐛 fix params.test_data_base in test and test_full configs #310
  • 🤖 GitHub Actions CI - pull_reqest to dev tests with NXF_VER latest-everything #310
  • 🤖 GitHub Actions CI - pull_reqest to master tests with NXF_VER 22.10.1 & latest-everything #310
  • 🤖 GitHub Actions CI - fail-fast set to false #310
  • 🐛 get to the bottom of index tests #278
  • ✨ Support for Bismark methylation extraction ignore and ignore_3prime parameters when ignore_r1 or ignore_3prime_r1 are greater than 0. #322
  • 🛠️ rename ignore -> ignore_r1 and ignore_3prime -> ignore_3prime_r1 params #322
  • 🐛 removed unused directory #297

Files

nf-core/methylseq-2.4.0.zip

Files (4.1 MB)

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Additional details

Related works

Is supplement to
https://github.com/nf-core/methylseq/tree/2.4.0 (URL)