nf-core/mag

View on GitHub

Assembly and binning of metagenomes

Stars: 321
Forks: 156
Open beginner issues: 0
Indexed issues: 78
Avg merge: 12h 59m
Merged PRs (30d): 5

Dominant language: Nextflow
License: MIT
Last GitHub push: Aug 1, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted

Beginner friendly Everything

Open All

78 open issues indexed

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

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/mag#1115 · Opened Sep 18, 2026
Pipeline won't launch when Zenodo is down (even without --run_checkm2) Open

bug fixed on dev

Difficulty 3/5 1-2 days Newbie friendliness 68/100

nf-core/mag#1112 · 1 comment · Opened Sep 10, 2026
Support BUSCO quality estimates for --dereplicate Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

nf-core/mag#1111 · 1 comment · Opened Sep 9, 2026
Add compleasm Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/mag#1107 · Opened Aug 31, 2026
CLI parameters will be cast to string with Nextflow>26.04 which breaks many of them Open

bug fixed on dev

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/mag#1101 · 1 comment · Opened Aug 12, 2026
ComeBin ignores the --min_contig_size Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/mag#1100 · 3 comments · Opened Aug 11, 2026
--gunc_database_type options are invalid Open

bug fixed on dev

Difficulty 3/5 1-2 days Newbie friendliness 58/100

nf-core/mag#1098 · 2 comments · 1 reaction · Opened Aug 11, 2026
Extract circular MAGs directly Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/mag#1097 · Opened Aug 7, 2026
the bin filename ${bin} does not match the expected format 'MEGAHIT-MetaBinner-group-612.([_[:alnum:]]+).fa'! Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/mag#1077 · 3 comments · Opened Jul 15, 2026
METABINNER_METABINNER can't cache some samples Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/mag#1052 · Opened Jun 17, 2026
COMEBIN taking forever Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/mag#1046 · 3 comments · Opened May 27, 2026
Create newcomer guidance documentation page Open

enhancement

Difficulty 1/5 Under an hour Newbie friendliness 15/100

nf-core/mag#1045 · Opened May 27, 2026
Additon of Fastplong Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/mag#1033 · 1 reaction · Opened May 6, 2026
Add skDER/CiDDER for bin dereplication Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/mag#1024 · Opened Apr 14, 2026
Add myloasm Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/mag#1023 · Opened Apr 14, 2026
[tracker] new tools Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 38/100

nf-core/mag#1022 · Opened Apr 14, 2026
Add `gunc_checkm_summary.tsv` table to `bin_summary.tsv Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/mag#982 · Opened Feb 13, 2026
Add DeepMAsED to the pipeline Open

enhancement fixed on dev

nf-core/mag#980 · 1 assignee · Opened Feb 11, 2026
BOWTIE2_ASSEMBLY_ALIGN fails with samtools "-@" option under conda profile Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/mag#978 · Opened Feb 8, 2026
Add dedicated parameters for Trimmomatic adapter clipping Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/mag#971 · Opened Jan 27, 2026
Count table after mapping reads back to the dereplicated MAGs Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/mag#955 · 2 comments · Opened Dec 3, 2025
Better document BUSCO run by default, and how to turn it off Open

enhancement

nf-core/mag#951 · 1 assignee · Opened Dec 2, 2025
GPU acceleration for COMEBin and SemiBin2 Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/mag#936 · 4 comments · Opened Nov 19, 2025
[tracker] improve testing datasets and databases Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 10/100

nf-core/mag#916 · Opened Nov 6, 2025
Make a small CheckM2 database for running tests Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/mag#915 · 3 comments · Opened Nov 6, 2025
Generate MGNify submission compatible metrics Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/mag#903 · 1 reaction · Opened Oct 28, 2025
Utilization of both old assemblies and new raw reads Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

nf-core/mag#887 · Opened Oct 20, 2025
Find CI test dataset for binner "COMEBin" & "MetaBinner" Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/mag#884 · 1 comment · Opened Oct 17, 2025
Low-complexity sequence filtering Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/mag#877 · 5 comments · Opened Oct 10, 2025
GENOMAD may fail when running with `conda` Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/mag#872 · Opened Sep 30, 2025
Improve environments of local modules Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/mag#868 · Opened Sep 23, 2025
Ancient DNA mode: Add pyDamage results to bin_summary.tsv Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/mag#833 · Opened Jun 22, 2025
Use hostile for host read removal Open

enhancement

nf-core/mag#822 · 7 comments · 1 assignee · Opened Jun 2, 2025
Refactor pipeline to only refer to params in entry workflow Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/mag#821 · 1 reaction · Opened Jun 2, 2025
Standardise pre-processing parameter flags between long and short reads Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/mag#806 · 1 reaction · Opened May 14, 2025
Add fairy for fast co-coverage estimation Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/mag#796 · 5 comments · 2 reactions · Opened May 8, 2025
QUAST_BINS can be very slow / Reconfigure BIN_SUMMARY table Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 32/100

nf-core/mag#789 · 1 comment · 1 reaction · Opened Apr 9, 2025
Replace QUAST custom modules with official nf-core ones Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/mag#748 · 6 comments · Opened Jan 20, 2025
Compress FASTA files with contigs and scaffolds using bgzip instead of gzip, to enable file indexing Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/mag#746 · 5 comments · Opened Jan 19, 2025
Ensure unique contig names across assemblies, for chaining pipeline with magmap Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/mag#742 · Opened Jan 6, 2025
Create a summary report Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/mag#728 · 1 comment · Opened Dec 10, 2024
Consider using Taxometer (From VAMB) for taxonomic classification of metagenomic contigs Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/mag#722 · 1 comment · 1 reaction · Opened Dec 3, 2024
Consider binette as alternative bin refinement tool Open

nf-core/mag#714 · 2 comments · 1 assignee · Opened Nov 13, 2024
--host_fasta_bowtie2index path taken for bowtie -S output file Open

bug

nf-core/mag#694 · 4 comments · 1 assignee · Opened Oct 16, 2024
Optional skipping of short-read input to Filtlong for large datasets Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 42/100

nf-core/mag#691 · 3 comments · Opened Oct 14, 2024
Generate taxprofiler samplesheet from mag Open

nf-core/mag#687 · 1 assignee · Opened Oct 10, 2024
Create a samplesheet for funcscan Open

enhancement

nf-core/mag#686 · 5 comments · 1 assignee · Opened Oct 10, 2024
Consider CarpeDeam for (ancient DNA) damage aware assembler Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/mag#650 · Opened Aug 12, 2024
Add module pyrodigal Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/mag#624 · Opened Jun 3, 2024
Enter at postbinning stage Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/mag#623 · 9 comments · Opened Jun 3, 2024

nf-core/mag

Get new issues in your inbox