Hi, since this is recently came up in a PR, it appears that nf-co.re/docs/contributing/contributor-types#… is ambigous, and (presumably) not handled consistently across pipelines. I was made aware that e.g. PR reviews constitute a contribution (not disagreeing there), however, when I checked a bunch of pipelines to find entries to c&p into my manifest, I noticed that some pipelines seem to not record those contributions. I think this is something that is easily forgotten, and I was wondering if that is something that e.g. could be automated with #CE5LG7WMB?

Got a suggestion, due to colleagues returning to pipelines with modules that download dbs from urls after a long time, and resume is broken. How do you all feel about a predownload workflow under workflows/ ? That would be execute-once (for user-selected dbs), and then the main workflow would only allow the _path versions of those parameters.

after a long delay due to our AWS outage and vacation, I will finally kick of the 4.1.0 template sync. Biggest template related change is probably a new pre-commit hook to help keep repos clean. Merge conflicts should be not too difificult this time (🤞🏻) (I put two common ones at the end of the blog post, more to come if you point them out). If you see something weird or are unsure about what to do, feel free to write here or ping me.

I need help with this error github.com/nf-core/variantbenchmarking/…/100267702399?pr=322 the container configs are updated with the template update 4.1.0, but linter is failing..I also dont really understand why we need those configs now 😄.

publishDir does not allow lists of maps anymore, so publishDir like hits will now fail:

publishDir = [
            [
                path: { "${params.outdir}/remove_redundancy/merge_families/full_msa/raw/mgnifam/${meta.id}/" },
                mode: params.publish_dir_mode,
                pattern: "*/full_msa/*",
                saveAs: { filename -> filename.tokenize('/').last() }
            ],
            [
                path: { "${params.outdir}/remove_redundancy/merge_families/hmm/raw/mgnifam/${meta.id}/" },
                mode: params.publish_dir_mode,
                pattern: "*/hmm/*",
                saveAs: { filename -> filename.tokenize('/').last() }
            ],
            [
                path: { "${params.outdir}/remove_redundancy/merge_families/generate_families_iteratively/${meta.id}/" },
                mode: params.publish_dir_mode,
                enabled: params.save_iterative_family_metadata,
                pattern: "*/*.*"
            ]
        ]

Is this wanted behaviour or a bug? What is the suggested way of writing these now? I don't like what the bots are proposing and cannot see any alternative:

publishDir = [
            path: { "${params.outdir}/remove_redundancy/merge_families" },
            mode: params.publish_dir_mode,
            saveAs: { filename ->
                def parts = filename.tokenize('/')
                if (parts.size() == 3 && parts[1] == 'full_msa') { return "full_msa/raw/mgnifam/${meta.id}/${parts[2]}" }
                if (parts.size() == 3 && parts[1] == 'hmm')      { return "hmm/raw/mgnifam/${meta.id}/${parts[2]}" }
                if (!params.save_iterative_family_metadata)      { return null }
                if (parts.size() == 2 && parts[1].contains('.')) { return "generate_families_iteratively/${meta.id}/${filename}" }
                return null
            }
        ]

Hello everybody, I am getting berserk writing SKILLS.md for everything I work on. Where would be the best place in an nf-core pipeline for a skills file instructing the agent what can be done with the output of the pipeline?

Hi! I’m currently working on the

provenancereport

pipeline and I could use some help with the repository setup. When the repository was initially created, it only had a

dev

branch. Following the nf-core documentation, I’ve managed to create the

TEMPLATE

branch, but I don’t have the permissions needed to create a

main

branch. I also tried creating a

master

branch so I could follow the available migration guide to convert it to

main

, but I don’t have permission to create that branch either. Would someone from the core team be able to help me create the

main

branch? Thanks!

I am a bit lost here. When I update the template from 4.0.2 to 4.1.0 I first hit the

ERROR ~ Cannot invoke method endsWith() on null object

as in github.com/nextflow-io/nextflow/issues/7474, solved that then as in https://nfcore.slack.com/archives/C04QR0T3G3H/p1788431565519489?thread_ts=1788428388.351539&cid=C04QR0T3G3H. However, the next issue is

ERROR ~ No such variable: task

... How to solve that one? Is it better to just wait for nextflow 26.04.7 thats might fix that? Edit: The above is for

NXF_VER=26.04.6 nextflow config -o json

, no issue with

NXF_VER=25.10.4 nextflow config -o json

Often that error is actually the fault of an invalid (too long/short) input tuple

How can there be a conflict for a PR from dev to master? 😱 github.com/nf-core/ampliseq/pull/1091 How can I fix that cleanly? 😬 Just resolve the conflict in the PR as usual on other PRs?

Looking for any and all tips and tricks from the community here! 🙏🏻 https://nfcore.slack.com/archives/C043UU89KKQ/p1790929501164579

Any wave-experts out there that could increase my confidence in merging this github.com/nf-core/epitopeprediction/pull/338?

Hi, a quick question. I've been refactoring rnasplice to match nfcore standard, fixed bugs etc. The pipeline was in an orphaned state. Do I consider myself a maintainer of the pipeline? Just to understand the level of engagement I'm expected to put into this. Thanks, and sorry for the silly question!

Hi! I come with a question... I made a small patch release, but forgot to run

bump-version

beforehand. Would it be okay to make a small PR to fix this, or should I make a new patch release instead?

Hi folks! Two questions for all you pipeline maintainers out there: 1. Does your pipeline have a custom logo / sticker? 2. If yes: is it listed on nf-co.re/stickers? Please make sure that they're added to github.com/nf-core/logos if your answers are

Yes

+

No

! ✨

RE: https://nfcore.slack.com/archives/CE6P95170/p1791365042101449 patch PRs incoming. feel free to merge them on your own, otherwise we will go through and merge them

I'm currently fixing the default arguments passed through config to the main imputation algorithm of phaseimpute. I'm wondering if it could be a good idea to add some nextflow arguments that the user could pass to the ext.args of each imputation process. Something like "opt_args_glimpse1" that would be added to

ext.args   = { "--impute-reference-only-variants --seed ${params.seed} ${params.opt_args_glimpse1}" }

This would allow users to fine tune algorithm without having to dive into all the configs files. Is it something that you do in other pipeline ?

First round of fixes is done. Now I will push the fix for the tower action.

There are a number of megatest failures. I described the temprary workaround and why this happens here: https://nfcore.slack.com/archives/CE9BJ6X6V/p1790870454114089?thread_ts=1790776381.828399&cid=CE9BJ6X6V

Hi, quick question about

processVersionsFromYAML

. Have you faced the issue where versions are written in the YAML as numbers, and something like x.10 becomes x.1 ? I'm having this issue with sed 4.10, which is reported in the YAML as 4.1, using the output:

tuple val("${task.process}"), val('sed'), eval('sed --version 2>&1 | head -n1 | sed "s/.* //"'), topic: versions, emit: versions_sed

got a bit delayed yesterday, so finnaly pushing the tower action fix. I would recommend against giving it a review, because it will trigger a full run on aws

I have received a bug report which I do not really understand, could someone take a look at this github.com/nf-core/genomeassembler/issues/238 and let me know what you think? My general impression is that the suggested cause for the bug is misleading, but I also do not really have a good understanding of what is causing concurrent modificiation exceptions, I would generally assume that the tests should catch that, but maybe this is some edge-case?

In #CE9MS66BS we already migrated to typed workflows, and full tests are failing because it seems to be using the v1 parser:

N E X T F L O W  ~  version 26.04.6
Pulling nf-core/mag:dev ...
downloaded from <https://github.com/nf-core/mag.git>
Downloading plugin nf-slack@0.5.0
Launching `<https://github.com/nf-core/mag>` [silly_descartes] - revision: 7fbb2153e3 [dev]
Slack plugin: Enabled with Bot notifications
WARN: Slack plugin: Failed to add reaction 'x': missing_scope (add reactions:write scope to your Slack app)
ERROR ~ Script compilation error
- file : /.nextflow/assets/.repos/nf-core/mag/clones/7fbb2153e338225380fe64d22148de7a044de899/main.nf
- cause: The LHS of an assignment should be a variable or a field accessing expression @ line 61, column 28.
       longreads_min_quality: Integer?
                              ^
1 error
-- Check 'nf-4I0ZPCLhvNJueH.log' file for details

How should we handle this correctly?

Hi, I'm preparing the 2.0.0 release. Could I get access to the AWSmegatests workspace on Seqera Platform, so I can follow the full-size test runs of rnasplice? Thanks!

Hi, I've opened the PR to merge dev into main for nf-core/rnasplice github.com/nf-core/rnasplice/pull/318. But it still requires the old "Prettier" status check, which no longer exists since the template moved to pre-commit, so the PR shows it as pending forever. Can anyone help me with this? Thanks!

Hi! I'd like to have your point of view concerning the integration of Nextflow pipelines (nf-core or not) into other Nextflow pipelines. I'm currently developing the new #C0C6WPPDT0R pipeline, and ideally I'd like to integrate: • github.com/ebi-pf-team/interproscan6 • github.com/nf-core/ncrnannotator Is it possible to integrate such pipelines through git submodules (or an equivalent)? Using something like nf-cascade would be last resort solution, if something else works. Thanks a lot!

we just released nf-core tools 4.2.0. It's not a very big release, but I will still test a few template update before kicking off a full sync, so don't get worried if your pipeline doesn't have the latest template PR yet 🙂

I have just made a mistake in nf-core/detaxizer: I pressed the "merge" button on a PR dev->master too early without correcting the release date (today...). While I am a maintainer of that pipeline, I seem to have restricted rights. Could I either get more power that I can fix that myself or could someone correct that? (Or maybe I overlooked another easy solution?) Here is what ideally would be changed github.com/nf-core/detaxizer/pull/112#…. I havent done the release yet, fortunately.

4.2.1 is out with a template update. Shout if you see anything weird. unfortunately, it seems it touched files in a way that they generate merge conflicts, but they shouldn't be too difficult/confusing, I will collect the most commonly found ones here: https://nf-co.re/blog/2026/tools-4_2_0#how-to-resolve-common-merge-conflicts-on-pipeline-sync-prs

Hi all, as some of you noticed, I have tried to run my tool to resolve the template updates without conflicts. In the process, I have created pairs of stacked PR drafts; I intend to curate them in the coming days. I have done this work earlier with good feedback from the community, yet this time I've noticed that it has brought a lot of confusion. Context - what is the goal Template updates have been relying on exact matches, not intentions. The best example would be YAML patching, which would be error-prone; however, we can instead describe exactly the core migration by knowing its structure (ex. update property

foo.bar

with value

baz

). I will not attempt another wide-scale update, and it is fair to close those draft PR. For the ones that will remain open, I will keep working on updates and request reviews (move things from draft) once I deem them ready.