Issues

• Magscot as alternative bin refinement tool

  enhancement
  nf-core/mag#1131 · Filter by author brovolia opened on Oct 23, 2026

• GTDB-Tk and CheckM/CheckM2 summaries name bins differently (with vs. without .fa)

  nf-core/mag#1117 · Filter by author erikrikarddaniel opened on Sep 26, 2026
  

• BUSCO batch mode leaks lineage state between bins: bin_summary.tsv mixes odb10/odb12.2, mislabels domains and misaligns columns

  nf-core/mag#1115 · Filter by author vagkaratzas opened on Sep 18, 2026
  3

• Pipeline won't launch when Zenodo is down (even without --run_checkm2)

  bugfixed on dev
  nf-core/mag#1112 · Filter by author clairedubin opened on Sep 10, 2026
  1

• Support BUSCO quality estimates for --dereplicate

  enhancement
  nf-core/mag#1111 · Filter by author erikrikarddaniel opened on Sep 9, 2026
  1

• Add compleasm

  enhancement
  nf-core/mag#1107 · Filter by author dialvarezs opened on Aug 31, 2026

• CLI parameters will be cast to string with Nextflow>26.04 which breaks many of them

  bugfixed on dev
  nf-core/mag#1101 · Filter by author cdiener opened on Aug 12, 2026 · 5.6.0
  1

• ComeBin ignores the --min_contig_size

  bugfixed on dev
  nf-core/mag#1100 · Filter by author cdiener opened on Aug 11, 2026
  3

• --gunc_database_type options are invalid

  bugfixed on dev
  nf-core/mag#1098 · Filter by author cdiener opened on Aug 11, 2026 · 5.6.0
  2

• Extract circular MAGs directly

  enhancement
  nf-core/mag#1097 · Filter by author prototaxites opened on Aug 7, 2026

• the bin filename ${bin} does not match the expected format 'MEGAHIT-MetaBinner-group-612.([_[:alnum:]]+).fa'!

  bug
  nf-core/mag#1077 · Filter by author jorondo1 opened on Jul 15, 2026
  3

• METABINNER_METABINNER can't cache some samples

  bug
  nf-core/mag#1052 · Filter by author jorondo1 opened on Jun 17, 2026

• COMEBIN taking forever

  nf-core/mag#1046 · Filter by author francesco-ricci opened on May 27, 2026
  4

• Create newcomer guidance documentation page

  enhancement
  nf-core/mag#1045 · Filter by author jfy133 opened on May 27, 2026

• Additon of Fastplong

  enhancement
  nf-core/mag#1033 · Filter by author MicroSeq opened on May 6, 2026

• Add skDER/CiDDER for bin dereplication

  enhancement
  nf-core/mag#1024 · Filter by author dialvarezs opened on Apr 14, 2026

• Add myloasm

  enhancement
  nf-core/mag#1023 · Filter by author dialvarezs opened on Apr 14, 2026
  

• [tracker] new tools

  enhancement
  nf-core/mag#1022 · Filter by author dialvarezs opened on Apr 14, 2026

• Add gunc_checkm_summary.tsv table to `bin_summary.tsv

  enhancement
  nf-core/mag#982 · Filter by author jfy133 opened on Feb 13, 2026

• Add DeepMAsED to the pipeline

  enhancementfixed on dev
  nf-core/mag#980 · Filter by author amizeranschi opened on Feb 11, 2026
  

• BOWTIE2_ASSEMBLY_ALIGN fails with samtools "-@" option under conda profile

  bug
  nf-core/mag#978 · Filter by author Ruiqi-CUB opened on Feb 8, 2026

• Add dedicated parameters for Trimmomatic adapter clipping

  enhancement
  nf-core/mag#971 · Filter by author Pranjal-Bioinfo opened on Jan 27, 2026

• Count table after mapping reads back to the dereplicated MAGs

  enhancement
  nf-core/mag#955 · Filter by author richrr opened on Dec 3, 2025
  2

• Better document BUSCO run by default, and how to turn it off

  enhancement
  nf-core/mag#951 · Filter by author jfy133 opened on Dec 2, 2025
  

• GPU acceleration for COMEBin and SemiBin2

  enhancement
  nf-core/mag#936 · Filter by author d4straub opened on Nov 19, 2025
  4