Published August 10, 2025 | Version 4.1.0
Software Open

nf-core/methylseq: Burrows Stardust

Creators

  • 1. @seqeralabs
  • 2. PeriMatrix IT Consultancy
  • 3. @imbforge
  • 4. Van Andel Institute
  • 5. Boehringer Ingelheim
  • 6. @MGXlab
  • 7. @ScilifelabDataCentre
  • 8. Altos Labs, Cambridge Institute of Science
  • 9. QBiC @qbicsoftware
  • 10. National Genomics Infrastructure
  • 11. @402s
  • 12. Human Technopole
  • 13. Seqera Labs
  • 14. MPI-CBG
  • 15. Seqera
  • 16. BIH/MDC Genomics Platform
  • 17. Cantu Lab @ UC Davis
  • 18. @dnanexus
  • 19. INRAE

Description

nf-core/methylseq 4.1.0

  • Highlights

    • Optional BWA-MEM2 support via --use_mem2 for BWA-Meth indexing and alignment
    • Nextflow requirement raised to 24.10.5
    • Broad module/template updates and CI hardening

  • New

    • Add --use_mem2 to enable the BWA-MEM2 algorithm in BWA-Meth
      • BWA-Meth modules updated to honor use_mem2
      • fasta_index_bismark_bwameth subworkflow updated to pass use_mem2

  • Improvements

    • Update template to nf-core/tools v3.3.2
    • General modules update
    • Add GitHub Actions CI for GPU test snapshot updates
    • Update AWS megatests workflow to use new CE org variables
    • Add Wave to ARM megatests

  • Fixes

    • FastQC output added twice to multiqc_ch
    • Broken documentation links
    • Update BWA-Meth container to fix bwa-mem2 installation

  • Testing

    • New test covering BWA-MEM2 indexing and alignment

  • Requirements

    • Nextflow >=24.10.5

  • Compatibility notes

    • Default behavior unchanged unless --use_mem2 is provided.

Full Changelog: https://github.com/nf-core/methylseq/compare/4.0.0...4.1.0

Files

nf-core/methylseq-4.1.0.zip

Files (4.0 MB)

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md5:a83e294df1a51472950db878c9b7d50b
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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/methylseq/tree/4.1.0 (URL)

Software

Repository URL
https://github.com/nf-core/methylseq