Issues

• Port RGI plots

  enhancement
  nf-core/funcprofiler#83 · Filter by author nickp60 opened on Oct 14, 2026

• Move to official bioconda containers for HUMAnN v4

  enhancement
  nf-core/funcprofiler#78 · Filter by author nickp60 opened on Aug 6, 2026 · V1.1

• SENSIBLE DEFAULTS

  enhancement
  Enhancement

  nf-core/funcprofiler#75 · Filter by author nickp60 opened on Aug 3, 2026
  4

• CAT_FASTQ: symlink fastq files when no merging needed

  enhancement
  nf-core/funcprofiler#70 · Filter by author funnell opened on Jul 30, 2026
  3

• Any opportunities to delete intermediate files?

  enhancement
  nf-core/funcprofiler#69 · Filter by author funnell opened on Jul 30, 2026
  6

• Consider adding SHOGUN support?

  enhancement
  nf-core/funcprofiler#36 · Filter by author miraep8 opened on Mar 31, 2026

• Benchmark ideal parameters for eggnog-mapper

  enhancement
  nf-core/funcprofiler#33 · Filter by author nickp60 opened on Mar 19, 2026

• Add merging/renaming functionality

  enhancement
  nf-core/funcprofiler#23 · Filter by author miraep8 opened on Mar 10, 2026

• Should we support aligning reads to annotated contigs?

  nf-core/funcprofiler#22 · Filter by author miraep8 opened on Mar 10, 2026
  1

• Add support for custom shortBRED annotation/custom DBs?

  enhancement
  nf-core/funcprofiler#19 · Filter by author miraep8 opened on Mar 10, 2026

• Decide whether to support long-reads

  enhancement
  nf-core/funcprofiler#18 · Filter by author nickp60 opened on Mar 9, 2026
  1