Burrows Stardust

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: 4.0.0...4.1.0