Just a hackathon update! Today we don't have anyone on-site (EMBL-EBI) working on #C07URFZF074, but @eparisis is working online on improving the outputs of the

update_families

subworkflow; specifically, coding the logic for it to also output

.faa

files per family, as done in the main workflow.

Hi! I'm Muskan, a final-year Biotech student. I'm a beginner but I know Python. I'd love to help with creating nf-tests for local modules. Can someone point me to a module that needs a test?

any interest in passing -O *.sto to hmmbuild so we can use the cons seq later for a curation by --hand?

✅ proteinfamilies/test_full completed successfully! 🎉 Run Name confident_gautier Duration 18m 14s Status ✅ Success Tasks Completed: 210 May 5, 2026 at 5:35 PM 🔗 View in Seqera Platform button

Did this run automatically from https://github.com/nf-core/proteinfamilies/pull/165 or did somebody manually start it? o.O

I think they run automatically now, whenever you get a ✅ on a PR that goes to

main

Are they pre-emptive AWS runs then, and I'll get my nf-core page output files right as it gets merged to main? Or will those run once again?

It'll run again on release (it needs to, as the website renders based on commit, and it'll be different post-merge). This is just to catch errors prior to release.

Gotcha!

Post-hackathon release 2.3.0 finally out! https://github.com/nf-core/proteinfamilies/releases/tag/2.3.0 Thank you @eparisis and @JuanFMx2 for joining :D The main changes are; having a compiled and compressed HMM library as an output per input sample, .faa files as outputs of the update mechanism, and the most important..! new pipeline logos :D

✅ proteinfamilies/test_full completed successfully! 🎉 Run Name infallible_woese Duration 15m 13s Status ✅ Success Tasks Completed: 210 May 6, 2026 at 7:01 AM 🔗 View in Seqera Platform button

✅ proteinfamilies/test_full completed successfully! 🎉 Run Name nostalgic_mayer Duration 17m 51s Status ✅ Success Tasks Completed: 210 Jun 9, 2026 at 8:11 AM

✅ proteinfamilies/test_full completed successfully! 🎉 Run Name silly_sanger Duration 16m 10s Status ✅ Success Tasks Completed: 210 Jun 9, 2026 at 12:11 PM

✅ proteinfamilies/test_full completed successfully! 🎉 Run Name wise_kirch Duration 11m 15s Status ✅ Success Tasks Completed: 210 Jun 9, 2026 at 1:57 PM

Hi everyone, I may be misunderstanding something, but I encountered an

OSError: [Errno 36] File name too long

while running

nf-core/proteinfamilies

on a large HRGM2 protein database. It occurs in

REMOVE_REDUNDANCY > MERGE_FAMILIES > MERGE_SEEDS

, where a component of ~80 similar families appears to be represented by a very long output filename. Is this a known limitation, and is there a recommended workaround besides

--skip_family_merging

? I can share the full log and

.command.sh

if helpful. If this is useful context, I wondered whether a short deterministic merged-family ID plus a mapping back to the member families might avoid the filename limit.

✅ proteinfamilies/test_full completed successfully! 🎉 Run Name soggy_nightingale Duration 15m 32s Status ✅ Success Tasks Completed: 210 Jul 24, 2026 at 2:56 PM

✅ proteinfamilies/test_full completed successfully! 🎉 Run Name cheeky_almeida Duration 14m 46s Status ✅ Success Tasks Completed: 210 Aug 10, 2026 at 2:33 PM

New pipeline version 2.5.0 out! with a bug fix for multi-sample runs that went through merging, along with some other fixes that @Yixuan Yang pointed out! Also allowing a new family generation algorithm,

mgnifam

, which promises to produce more refined models and alignments due to its iterative nature (future work to benchmark against current standard way of producing families, to quantify stats). Enable it with

--family_generation_algorithm iterative

See the changelog here: github.com/nf-core/proteinfamilies/…/2.5.0

If you want to find more about the

mgnifam

tool, here you go: github.com/vagkaratzas/mgnifam It's the core family generation algorithm of our MGnifams pipeline in EBI

✅ proteinfamilies/test_full completed successfully! 🎉 Run Name special_moriondo Duration 10m 54s Status ✅ Success Tasks Completed: 210 Aug 11, 2026 at 9:26 AM

❌ proteinfamilies/test_full failed 😿 Run Name magical_colden Duration 33.6s Status ❌ Failed Error Message

Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/proteinfamilies>, projectDir: /.nextflow/assets/.repos/nf-core/proteinfamilies/clones/0bad731199b96aec78abbaef6f06212d7d215678, commitId: 0bad731199b96aec78abbaef6f06212d7d215678, revision: dev, startTime: 2026-09-30T19:26:12.678939426Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/proteinfamilies>' -name magical_colden -params-file '<https://api.cloud.seqera.io/ephemeral/UaBSR3oCee7QOpMK9A_vLQ.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$Preview@41c7ef69, enable:nextflow.NextflowMeta$Features@15e86d24, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/proteinfamilies/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

nextflow run '<https://github.com/nf-core/proteinfamilies>' -name magical_colden -params-file '<https://api.cloud.seqera.io/ephemeral/UaBSR3oCee7QOpMK9A_vLQ.json>' -with-tower -r dev -profile test_full

Sep 30, 2026 at 7:26 PM

❌ proteinfamilies/test_full failed 😿 Run Name friendly_franklin Duration 12.5s Status ❌ Failed Error Message

Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/proteinfamilies>, projectDir: /.nextflow/assets/.repos/nf-core/proteinfamilies/clones/0bad731199b96aec78abbaef6f06212d7d215678, commitId: 0bad731199b96aec78abbaef6f06212d7d215678, revision: dev, startTime: 2026-10-01T08:57:20.294977875Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/proteinfamilies>' -name friendly_franklin -params-file '<https://api.cloud.seqera.io/ephemeral/fdvzLqVRiXj0cLgKWebKCw.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$Preview@10ef09e3, enable:nextflow.NextflowMeta$Features@776d50d6, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/proteinfamilies/work-dev, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

nextflow run '<https://github.com/nf-core/proteinfamilies>' -name friendly_franklin -params-file '<https://api.cloud.seqera.io/ephemeral/fdvzLqVRiXj0cLgKWebKCw.json>' -with-tower -r dev -profile test_full

Oct 1, 2026 at 8:57 AM

Ignore, I blame AWS :p

❌ proteinfamilies/test_full failed 😿 Run Name mad_mercator Duration 35.8s Status ❌ Failed Error Message

Missing process or function paramsSummaryLog([[:], repository: <https://github.com/nf-core/proteinfamilies>, projectDir: /.nextflow/assets/.repos/nf-core/proteinfamilies/clones/318acd54eb9c679553338b2db46313bb469d03d1, commitId: 318acd54eb9c679553338b2db46313bb469d03d1, revision: 2.6.0, startTime: 2026-10-01T10:29:44.098254152Z, endTime: null, duration: null, container: {}, commandLine: nextflow run '<https://github.com/nf-core/proteinfamilies>' -name mad_mercator -params-file '<https://api.cloud.seqera.io/ephemeral/wPyWhHi5e7x7Yb3tac_pMg.json>' -with-tower -r 318acd54eb9c679553338b2db46313bb469d03d1 -profile test_full, nextflow: nextflow.NextflowMeta(version:26.04.6, build:12646, timestamp:09-07-2026 18:49 UTC, preview:nextflow.NextflowMeta$Preview@67e255cf, enable:nextflow.NextflowMeta$Features@1bb90d4d, strictModeEnabled:false, moduleBinariesEnabled:false), success: false, workDir: /nf-core-awsmegatests/work/proteinfamilies/work-318acd54eb9c679553338b2db46313bb469d03d1, launchDir: /, profile: test_full]) -- Did you mean 'paramsSummaryLog' instead?

Command Line

nextflow run '<https://github.com/nf-core/proteinfamilies>' -name mad_mercator -params-file '<https://api.cloud.seqera.io/ephemeral/wPyWhHi5e7x7Yb3tac_pMg.json>' -with-tower -r 318acd54eb9c679553338b2db46313bb469d03d1 -profile test_full

Oct 1, 2026 at 10:30 AM

New release 2.6.0 (Tungsten Raven) out! See the changelog here: github.com/nf-core/proteinfamilies/releases#… Thanks to @Daniel Lundin and @Joon Klaps for the reviews! This one was the last metal-animal named release. Spoiler alert; next one is going to be a breaking release with little things I've been putting away for a while. So going for 3.0.0, with a naming twist, soon soon. Because who wants to be boring, right @James Fellows Yates? :P

✅ proteinfamilies/test_full completed successfully! 🎉 Run Name zen_lichterman Duration 17m 49s Status ✅ Success Tasks Completed: 210 Oct 1, 2026 at 11:04 AM

❌ proteinfamilies/test_full failed 😿 Run Name chaotic_picasso Duration 1.8s Status ❌ Failed Error Message

Script compilation error
- file : /.nextflow/assets/.repos/nf-core/proteinfamilies/clones/700d0e1f497651a9abdc5cac78bcd0df656b8414/main.nf
- cause: The LHS of an assignment should be a variable or a field accessing expression @ line 73, column 21.
       multiqc_config: Path?
                       ^

1 error

Command Line

nextflow run '<https://github.com/nf-core/proteinfamilies>' -name chaotic_picasso -params-file '<https://api.cloud.seqera.io/ephemeral/K5abSIh42tZ2DiL7doIcqg.json>' -with-tower -r dev -profile test_full

Oct 17, 2026 at 2:25 PM

depictio Depictio dashboard for proteinfamilies: feedback wanted Depictio (open source, from EMBL) turns the output of a workflow run into an interactive dashboard you can share, so nobody has to write a Shiny or Streamlit app for each project. Point a template at any run of a pipeline and you get the same dashboard, which you can edit (UI & YAML), version and comment. 🧪 The proteinfamilies dashboard template shows how the sequences cluster into families, family size and conservation, the family alignment and the profile HMM logo. 🙌 We need your help! Feedback and ideas welcome in #C0AFS06G9HR (all templates and details there) or in the proteinfamilies GitHub discussion. @Evangelos Karatzas 😎

<!channel> Do have a look at the above. I'm sure you will appreciate ;)

Depictio is great 🙂. Good stuff @Thomas Weber!