made a u-turn decision and decided to only test the container build functionality with the new container commands, but not changing anything of the structure of the main.nf for now. makes it easier to roll out hopefully https://github.com/nf-core/tools/pull/3954/changes/be61d6bbc858a6c0e4b0ec5b770d60869b3a7980 but will merge now

The CI in #CJRH30T6V uses the latest dev from #CE5LG7WMB, but the linting is broken because that enforces

meta_containers

. What’s the recommended action?

FYI, I had some extra Claude usage over the 4th, and had Fable until today, and tried to come up with a non-bioinformatics-related coding problem to let it churn on. So tree-sitter-nextflow now parses all of nf-core/modules successfully 🎉 But what this really means is we can use ast-grep for nf-core tools linting: github.com/nf-core/tools/pull/4377 Which lets us have this simple yaml per rule with the regex/syntax and write transformations etc. Stack of PRs

└─ #4377 Add AST-grep lint foundations
      └─ #4381 Migrate pipeline lint rules to AST-grep
         └─ #4378 Bump tree-sitter-nextflow parser pin
            └─ #4379 Flag legacy versions.yml topic outputs
               └─ #4380 Flag legacy versions emits

Noticed that in the stats page, the pipelines were weirdly sorted, and then I also noticed some corrupt release data, as #C0905QCFTPE was released (for a couple of months) but wasn’t tracked on the stats page. github.com/nf-core/stats/pull/139

trying out codspeed to measure our CLI speed (will hopefully soon get better): https://github.com/nf-core/tools/pull/4384

⚡ https://github.com/nf-core/tools/pull/4383 (give me reviews, if you want the faster CLI start ups winking cowboy)

Need to disable the code quality thing before GitHub tries to start charging us

I wish they'd say which single repository it is that has it enabled! shakefist

@mashehu any idea on why github regular runners don't generate MultiQC images cf https://nfcore.slack.com/archives/C049MBCEW06/p1784188552447639 this is outside of nf-core, but still nf-core adjacent, and I would say it's mainly a problem of a missing lib in the runner, but I am unsure about what is actually used there or what we do use on our side

Any idea why the github CI is failing here: github.com/nf-core/chipseq/…/88761230990?pr=530 ?

Regarding https://nfcore.slack.com/archives/CE6P95170/p1784904402855599?thread_ts=1784904402.855599&cid=CE6P95170 My main point was that a GitHub app hands out an installation token that by default is valid for one hour and scoped to the repository you request it for. Whereas a personal access token is valid until it expires or you remove it. This gives malicious actors much more time to exploit it. Within workflows you can also request the default GitHub token with different kinds of permissions. I'd have to study what the bot is supposed to do, to make more specific recommendations. I also have an agent skill for a security conscious review of GH workflows. I'll dig that up when I'm not on the phone.

This CI run merged even with a failing test: github.com/nf-core/modules/pull/12461 Fixing in https://github.com/nf-core/modules/pull/12471

new merge queue in #CM46YC6BZ https://github.com/bioconda/bioconda-recipes/pull/68020

Gave rich-codex a lick of paint and released v1.3.0 - github.com/ewels/rich-codex/…/v1.3.0 Might hopefully make it a little less annoying to work with 😅

Hi folks! Are we meeting today?

Why does

github_actions

seem to add 👀 reaction to issue comments on GitHub? (at least in

tools

repo)

Is the nf-core-bot not working to update gpu snapshots at the moment, or am I just failing to summon it? github.com/nf-core/modules/pull/12797

<!subteam^S08LAB76NBU> ok if I merge in github.com/nf-core/tools/pull/4460? @Yuxin Ning are you around to check and give a ✅ please if you're happy?

Just stumbled across github.com/reviewdog/action-suggester Takes a dirty git diff on a GitHub Actions runner (generated however) and turns it into comments with suggestions on a PR. Where have you been all my life?! Wonder if we could use this for

nf-core lint --fix

, even prettier etc? Might be a more elegant solution than messing around with complex GitHub actions permission sets and token handling? Only downside I guess is if it makes a lot of comments.

@nf-core fix linting

does everything in one pass, the above might require a lot of clicking for a lot of changes.

Quick update: I will be back at work Wednesday 30th. So you have until then to slip in all the things I am picky about 😉

I wrote a new GitHub actions workflow for MultiQC last night that can generate a report and then post a comment with a link to the actions artefact. To my surprise, you can open the artefact URL in a new tab and it actually renders as HTML properly (apparently this is a relatively new feature in GHA). It works beautifully. Is there anything we can do with this concept in the nf-core / Nextflow world? 🤔

hmm, wonder if stuff might be about to start breaking.. 😬

im-back-kate-mckinnon-gif-by-saturday-night-live.gif

#C07URFZF074 AWS test_full fired: cloud.seqera.io/orgs/…/logs but got an error. Seems to have pulled nf-schema@3.0.0 despite the 2.7.2 pin of the pipeline, and fails with:

Missing process or function paramsSummaryLog

Also throws a warning about the Slack plugin:

WARN: Slack plugin: Failed to add reaction 'x': missing_scope (add reactions:write scope to your Slack app)

Hello everyone, I have a question about PR size . i am trying to integrate sourmash in taxprofiler and my PR is flagged by the size labeler: "`message_if_xl: This PR exceeds the recommended size of 1000 lines. Please make sure you are NOT addressing multiple issues with one PR. Note this PR might be rejected due to its size.` Any thoughts about this? is this just a warning or should i split it up?

if only we had a

machine god

to fix the failing pipelines on AWS :D

The "Labeler" check on the nf-core/modules repository seems to be failing on every PR at the moment

hi all, Some odd behavior for a CI test (github.com/nf-core/chipseq/…/115002633197). test with nextflow 25.10.4 fails due to

No space left on device

on runner, while test with latest everything runs smooth. Also runs smooth on my local machine. any idea what I'm missing?

nf-core td ls

is not grepable because it asks for another user input. Would be awesome and helpful to also be able to pass that in somehow, so you can also pipe greps 😄