Issues

• Update chromograph to use Seqera Containers

  nf-core/modules#13593 · Filter by author paulinefx opened on Nov 4, 2026
  

• Update chelae/trim to use Seqera Containers

  nf-core/modules#13591 · Filter by author paulinefx opened on Nov 4, 2026
  

• Update checkv/downloaddatabase, checkv/endtoend, checkv/updatedatabase to use Seqera Containers

  nf-core/modules#13590 · Filter by author paulinefx opened on Nov 4, 2026
  

• Update centrifuger/build, centrifuger/centrifuger, centrifuger/quantification to use Seqera Containers

  nf-core/modules#13589 · Filter by author paulinefx opened on Nov 4, 2026
  

• Update ataqv/ataqv, ataqv/mkarv to use Seqera Containers

  nf-core/modules#13582 · Filter by author paulinefx opened on Nov 4, 2026
  

• Update ariba/getref, ariba/run to use Seqera Containers

  nf-core/modules#13570 · Filter by author paulinefx opened on Nov 4, 2026
  1

  

• new module: hamronization/resfinder

  new module
  nf-core/modules#13563 · Filter by author pabloestepaa opened on Nov 4, 2026
  1

  

• freyja/variants: FASTA index (.fai) is not an input, so FREYJA_VARIANTS fails on S3-backed work dirs

  nf-core/modules#13562 · Filter by author stefanoboriero opened on Nov 4, 2026

• Update anota2seq/anota2seqrun to use Seqera Containers

  nf-core/modules#13551 · Filter by author paulinefx opened on Nov 2, 2026
  

• Update antismash/antismashlite, antismash/antismashlitedownloaddatabases to use Seqera Containers

  nf-core/modules#13550 · Filter by author paulinefx opened on Nov 2, 2026
  

• Update amplify/predict to use Seqera Containers

  nf-core/modules#13547 · Filter by author paulinefx opened on Nov 2, 2026
  

• update module: NACHO/QC and NACHO/NORMALIZE

  nf-core/modules#13531 · Filter by author mcanouil opened on Nov 2, 2026

• [FEATURE] Add failed-reads BAM input to trgt/genotype

  update module
  Enhancement

  nf-core/modules#13520 · Filter by author alkc opened on Oct 31, 2026
  

• new module: fastvep/annotate

  new module
  nf-core/modules#13514 · Filter by author DylanMHouse opened on Oct 30, 2026
  

• ivar/trim directs log info to stderr resulting in blank log files

  bug
  nf-core/modules#13499 · Filter by author cjjossart opened on Oct 29, 2026

• new module: WormCat/batch, WormCat/enrich

  new module
  nf-core/modules#13497 · Filter by author DanHUMassMed opened on Oct 29, 2026
  

• new module: fairbioheaders (combine, verify, convert, validate)

  nf-core/modules#13491 · Filter by author adamjohnwright opened on Oct 29, 2026
  2

• new modules for metaSMASH, as an efficient alternative to antiSMASH

  new modulewishlist
  nf-core/modules#13489 · Filter by author amizeranschi opened on Oct 29, 2026

• new module: fgumi/realign

  new modulewishlist
  nf-core/modules#13488 · Filter by author matthdsm opened on Oct 29, 2026
  1

• new module: spectre/cnvcaller

  new module
  nf-core/modules#13481 · Filter by author DylanMHouse opened on Oct 28, 2026
  

• new subworkflow: fasta_binning_metabinner

  new subworkflowwishlist
  nf-core/modules#13463 · Filter by author vagkaratzas opened on Oct 26, 2026

• new module: metabinner/metabinner

  new modulewishlist
  nf-core/modules#13462 · Filter by author vagkaratzas opened on Oct 26, 2026

• new module: metabinner/genkmer

  new modulewishlist
  nf-core/modules#13461 · Filter by author vagkaratzas opened on Oct 26, 2026

• bam_telomere_estimation: TELOMEREHUNTER runs for only one sample (combine() yields a single-item queue channel)

  nf-core/modules#13434 · Filter by author adamrtalbot opened on Oct 21, 2026
  1

• Tests should create fixture files with collectFile instead of writing to launchDir or moduleDir

  good first issue
  nf-core/modules#13423 · Filter by author mahesh-panchal opened on Oct 20, 2026
  2