Issues

• Do the TIDYVERSE_SPLITFEATURECOUNTS and TIDYVERSE_JOINFEATURECOUNTSACCNO joins in DuckDB to bound memory

  enhancement
  nf-core/magmap#283 · Filter by author erikrikarddaniel opened on Oct 15, 2026 · Magmap 1.4
  

• Skip the separate BBMap index task with --genomeset_mode sample

  enhancement
  nf-core/magmap#282 · Filter by author erikrikarddaniel opened on Oct 15, 2026 · Magmap 1.4
  

• Support input of genomes from nf-core/mag

  enhancement
  nf-core/magmap#280 · Filter by author erikrikarddaniel opened on Oct 14, 2026
  1

  

• Save unaligned reads and write nf-core/taxprofiler input files

  enhancement
  nf-core/magmap#278 · Filter by author erikrikarddaniel opened on Oct 13, 2026

• Update the metro map with gffread and Bakta

  nf-core/magmap#269 · Filter by author erikrikarddaniel opened on Oct 6, 2026

• Accept Apptainer in the container selection of the local modules

  nf-core/magmap#265 · Filter by author erikrikarddaniel opened on Oct 1, 2026

• Report selected remote genomes missing from the NCBI assembly summaries

  nf-core/magmap#263 · Filter by author erikrikarddaniel opened on Oct 1, 2026

• Eukaryotic taxonomy/completeness metadata sources (GTDB/CheckM/GTDB-Tk equivalents)

  nf-core/magmap#241 · Filter by author erikrikarddaniel opened on Aug 13, 2026 · Magmap 1.4

• Add a eukaryotic gene caller (TransDecoder/MetaEuk) for transcriptomes/genomes lacking annotation

  nf-core/magmap#240 · Filter by author erikrikarddaniel opened on Aug 13, 2026 · Magmap 1.4

• Support eukaryotic metatranscriptomics via MMETSP transcriptome references

  nf-core/magmap#239 · Filter by author erikrikarddaniel opened on Aug 13, 2026 · Magmap 1.4

• Document potential differences in annotation tool version

  bug
  nf-core/magmap#229 · Filter by author erikrikarddaniel opened on Aug 4, 2026

• Add "instrain"?

  enhancement
  nf-core/magmap#184 · Filter by author erikrikarddaniel opened on Feb 24, 2026
  1

• Add eggnog-mapper and KOfamscan

  enhancement
  nf-core/magmap#164 · Filter by author danilodileo opened on Oct 22, 2025

• Allow user to avoid some steps in the pipeline when having a concatenated file ready

  enhancement
  nf-core/magmap#87 · Filter by author danilodileo opened on Oct 16, 2024
  

• Scan genomes with hmm profiles like in metatdenovo

  enhancement
  nf-core/magmap#34 · Filter by author erikrikarddaniel opened on Nov 16, 2023