Issues

• RGI_MAIN completes with exit 0 and truncated output after sub-process OOM kill

  bug
  nf-core/funcscan#551 · Filter by author dedewantstocode opened on Sep 28, 2026

• MultiQC report not displaying all all samples for bakta/prokka

  bug
  nf-core/funcscan#544 · Filter by author jasmezz opened on Aug 28, 2026

• prodigal process expects gzipped file

  bug
  nf-core/funcscan#541 · Filter by author moritzbuck opened on Jul 28, 2026

• ARG gene symbols are not standardized across tools in hAMRonization summary, making cross-tool comparison difficult

  enhancement
  nf-core/funcscan#525 · Filter by author OriolGEM opened on Apr 16, 2026
  4

• AMPCOMBI2_PARSETABLES error during stage-out with process.stageOutMode = 'move' -- "mv: cannot stat 'XYZ': No such file or directory"

  bug
  nf-core/funcscan#524 · Filter by author amizeranschi opened on Apr 5, 2026

• Add BiG-SCAPE

  enhancement
  nf-core/funcscan#509 · Filter by author juanmobovi opened on Dec 9, 2025
  2

  

• Bug in ARG + taxonomy merging

  bugrequires-upstream-fix
  nf-core/funcscan#491 · Filter by author jasmezz opened on Aug 14, 2025
  3

• Fix eventual ampcombi_parsetables crash

  enhancementrequires-upstream-fix
  nf-core/funcscan#489 · Filter by author jasmezz opened on Jul 22, 2025

• Update argNorm to current version

  enhancement
  nf-core/funcscan#487 · Filter by author jasmezz opened on Jul 17, 2025
  1

  

• Add support for reading external InterProScan results as pipeline input

  enhancement
  nf-core/funcscan#485 · Filter by author amizeranschi opened on Jul 9, 2025

• Integrate the existing eggNOG-mapper module into the pipeline

  enhancement
  nf-core/funcscan#473 · Filter by author amizeranschi opened on Apr 13, 2025

• Add support for generating mmseqs taxonomy reports

  enhancement
  nf-core/funcscan#466 · Filter by author amizeranschi opened on Mar 21, 2025
  2

• How to speed up MMseqs2 taxonomy assignment with GTDB database on large contigs?

  question
  nf-core/funcscan#424 · Filter by author lucianhu opened on Oct 18, 2024
  1

• A uniform input for all tools in each screening workflow

  enhancement
  nf-core/funcscan#385 · Filter by author m3hdad opened on Jun 5, 2024
  2

• Add module: resfinder

  enhancement
  nf-core/funcscan#330 · Filter by author jasmezz opened on Jan 23, 2024

• Adapt deepBGC to use GPUs

  enhancement
  nf-core/funcscan#326 · Filter by author Darcy220606 opened on Dec 19, 2023
  4

• Add pharokka to nf-core/funcscan

  feature-request
  nf-core/funcscan#329 · Filter by author CarsonJM opened on Dec 15, 2023
  

• Benchmarking tests showing resource values are suboptimal

  buglow-priority
  nf-core/funcscan#292 · Filter by author jfy133 opened on Jul 5, 2023

• Consider adding annotation tools to MultiQC report

  enhancement
  nf-core/funcscan#277 · Filter by author jfy133 opened on May 24, 2023
  

• Consider passing the annotation tool output to modules input for more standardization

  nf-core/funcscan#179 · Filter by author Darcy220606 opened on Dec 21, 2022