Just FYI @Danilo Di Leo @Daniel Lundin you tagged your release wrong in GitHub

Should be just

1.0.0

not

v1.0.0

Ops! I will correct it now!

See point 1.3 here

Hi! I know the pipeline currently expects GFFs in Prokka format, but I've been using Bakta annotation and ran into some column/attribute mismatches in the annotation module. I modified

NFCORE_MAGMAP:MAGMAP:PROKKAGFF2TSV

locally to be robust to missing columns (like

ec_number

) and to check for Bakta's

Dbxref

format. It works for Bakta now and stays compatible with Prokka. Do you think this is of general interest? If so I could create a pull request

For the hackathon: I started doing the template update for the pipeline and will address https://github.com/nf-core/magmap/issues/182 (

nextflow lint

) in the same PR. Will then turn to https://github.com/nf-core/magmap/issues/185.

I just updated the milestones a bit. I removed 1.0.1 since 1.1.0 will come earlier. (I moved all 1.0.1 issues to 1.1.0 except #87 that didn't seem urgent enough to me.) Let's aim to release https://github.com/nf-core/magmap/issues?q=is%3Aissue%20state%3Aopen%20milestone%3A%22Magmap%201.1.0%22 in March.

@Danilo Di Leo or whoever feels inclined: PR to review: https://github.com/nf-core/magmap/pull/188

I think we should release soon. Of the issues that are planned for 1.1.0 I'd like to do "Move genome_accno into count tables" but the others can be postponed, in my opinion.

Hi! I am running

magmap

with

-profile docker

and I have my own genome files

.fna

and

.gff

in the

genomeinfo.csv

. I am getting an error with

NFCORE_MAGMAP:MAGMAP:PROKKAGFF2TSV

where the

ec_number

columnn is missing. The

.gff

file was downloaded from NCBI and I joined it. Any idea on what could be wrong?

I have a question about this pipeline. Is it suitable for pure genomes (not metagenomic bins)? If not, from a conceptually level what makes this pipeline suitable for only metagenomic MAGs and not single-organism genome assemblies?

✅ magmap/test_full completed successfully! 🎉 Run Name suspicious_church Duration 1h 9m 45s Status ✅ Success Tasks Completed: 65 May 28, 2026 at 1:31 PM

🎉 nf-core/magmap v1.1.0 is out! Highlights: • Per-sample genome sets — each sample can now have its own set of reference genomes • Genome accession numbers added to counts tables • Fix for Bakta GFF compatibility • Fix for samtools output saving • Fix for

--indexes

accepting a proper list • Template updated to 4.0.2 Thanks to all contributors! Full changelog: https://github.com/nf-core/magmap/releases/tag/1.1.0

Hello, I am running the pipeline with a reference genome that was automatically annotated using RAST annotation server (fna and gff files). The pipeline runs well until FeatureCount where I got this error. Any idea how to go through it?

<!channel>: The pipeline is published in Bioinformatics: academic.oup.com/bioinformatics/…/8731927?…

✅ magmap/test_full completed successfully! 🎉 Run Name mad_kare Duration 1h 25m 2s Status ✅ Success Tasks Completed: 65 Jul 24, 2026 at 3:54 PM

✅ magmap/test_full completed successfully! 🎉 Run Name intergalactic_hilbert Duration 1d 15h 40m 8s Status ✅ Success Tasks Completed: 67 Aug 7, 2026 at 8:22 AM

Version 1.2.0 released: github.com/nf-core/magmap/…/1.2.0! The key points are: • Add a mechanism that makes it possible to prefer one genome over another for a single species • Add Bakta as alternative to Prokka • Write summary tables also in Parquet format Big thanks to @Rike Hanssen and @Evangelos Karatzas for release reviews, and several others for reviews along the way!

✅ magmap/test_full completed successfully! 🎉 Run Name chaotic_ampere Duration 1h 13m 10s Status ✅ Success Tasks Completed: 67 Aug 11, 2026 at 10:06 AM

✅ magmap/test_full completed successfully! 🎉 Run Name adoring_nightingale Duration 1h 9m 34s Status ✅ Success Tasks Completed: 67 Aug 11, 2026 at 10:34 AM

Hi, I ran magmap 1.2.0 to map two metatranscriptomes to GTDB release 226 and this worked flawlessly. However, when I add samples (currently trying with 12),

BBMAP_ALIGN

requires copious memory. I used > 15,000 core hours on

BBMAP_ALIGN

alone and only 3/12 finished. I used the parameter

sequence_filter

in combination with

SILVA_138.1_allrRNAref_NR99_tax.fasta

to try and reduce memory usage. Are there other things I could try? I am considering to lower the number of metatranscriptomes from 12 to 6 and try again. With 12 meta-t's I am mapping to 18,862 genomes, but this number goes down when lowering the no. of samples.

I'm using magmap 1.2.0 to map my shotgun metagenomes back to a small set of custom reference assemblies (using the genomeinfo argument). Is there a way to break down the mapping coverage by reference name rather than just overall for each sample? I don't see that particular break down in any of the files in summary_tables.

❌ magmap/test_full failed 😿 Run Name sad_volhard Duration 22.9s Status ❌ Failed Error Message

Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/magmap>, projectDir: /.nextflow/assets/.repos/nf-core/magmap/clones/e5a0b17491329265116f2f1d75b0de93885b6354, commitId: e5a0b17491329265116f2f1d75b0de93885b6354, revision: dev, startTime: 2026-10-07T08:10:13.499907907Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/magmap>' -name sad_volhard -params-file '<https://api.cloud.seqera.io/ephemeral/bCbuYCOz1ogQancHbvqOOQ.json>' -with-tower -r dev -profile test_full, nextflow: nextflow.NextflowMeta(version:26.04.6, build:12646, timestamp:09-07-2026 18:49 UTC, preview:nextflow.NextflowMeta$Preview@524241d9, enable:nextflow.NextflowMeta$Features@6f55aef7, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/magmap/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

nextflow run '<https://github.com/nf-core/magmap>' -name sad_volhard -params-file '<https://api.cloud.seqera.io/ephemeral/bCbuYCOz1ogQancHbvqOOQ.json>' -with-tower -r dev -profile test_full

Oct 7, 2026 at 8:10 AM

❌ magmap/test_full failed 😿 Run Name prickly_ritchie Duration 23.2s Status ❌ Failed Error Message

Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/magmap>, projectDir: /.nextflow/assets/.repos/nf-core/magmap/clones/ee96d68b82e05736542761c8f1f44578270863f6, commitId: ee96d68b82e05736542761c8f1f44578270863f6, revision: dev, startTime: 2026-10-07T10:02:46.651494793Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/magmap>' -name prickly_ritchie -params-file '<https://api.cloud.seqera.io/ephemeral/l5SuGRIa0wZxTSWSAEkwfw.json>' -with-tower -r dev -profile test_full, nextflow: nextflow.NextflowMeta(version:26.04.6, build:12646, timestamp:09-07-2026 18:49 UTC, preview:nextflow.NextflowMeta$Preview@1d9295e2, enable:nextflow.NextflowMeta$Features@4b708c16, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/magmap/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

nextflow run '<https://github.com/nf-core/magmap>' -name prickly_ritchie -params-file '<https://api.cloud.seqera.io/ephemeral/l5SuGRIa0wZxTSWSAEkwfw.json>' -with-tower -r dev -profile test_full

Oct 7, 2026 at 10:03 AM

✅ magmap/test_full completed successfully! 🎉 Run Name hungry_wozniak Duration 1h 12m 51s Status ✅ Success Tasks Completed: 65 Oct 8, 2026 at 12:08 AM

magmap 1.3.0 released: github.com/nf-core/magmap/…/1.3.0 Nothing revolutionary, but faster to start, a few bug fixes and other improvements. Thanks @Maxime Garcia, @mashehu, @Lea Picard (leapfroggie_), @Diego Alvarez Saravia, @piplus2, @Niklas Schandry, @Evangelos Karatzas, @kathryn.murie, @Louis Le Nézet, @Joon Klaps and @Danilo Di Leo for code and reviews!

✅ magmap/test_full completed successfully! 🎉 Run Name astonishing_murdock Duration 1h 14m 14s Status ✅ Success Tasks Completed: 65 Oct 8, 2026 at 12:33 PM

Bug fix release 1.3.1 out: github.com/nf-core/magmap/…/1.3.1 Thanks @mashehu, @piplus2 and @Ram!

❌ magmap/test_full failed 😿 Run Name condescending_cori Duration 2.4s Status ❌ Failed Error Message

No signature of method: nextflow.script.ScriptBinding.params() is applicable for argument types: () values: []
Possible solutions: getParams(), setParams(java.util.Map), setParams(java.util.Map, boolean), stream(), equals(java.lang.Object), print(java.io.PrintWriter)

Command Line

nextflow run '<https://github.com/nf-core/magmap>' -name condescending_cori -params-file '<https://api.cloud.seqera.io/ephemeral/y2jH-6Oe-H8uRjEhwzMA7Q.json>' -with-tower -r 839660084e48d682f70bed4e535f2a11a756638a -profile test_full

Oct 22, 2026 at 9:45 AM