---
title: nf-core/maintainers meeting notes 2023
tags: meetings,maintainers,2023
---

## 2023-12-15 - Cancelled

### Agenda

- Improvement on the modules regarding multiple meta maps (Wait until Mahesh is a maintainer, or until we picked up his brain)
- Thoughts on cmd for versions output -> https://github.com/nf-core/rnaseq/pull/1115

## 2023-11-24

### Agenda

- nf-test:
- modules now require nf-test (Simon Pearce) - only warning now
- We absolutely should snapshot version
- Handeling large scale changes, i.e. switching to environment.yml (James):
- tools are not released yet to handle this
- docs are not up to date
- CODEOWNER on modules:
- Auto-request reviews
- Ops and teams on GitHub (Edmund):
- POSTPONED: Improvement on the modules regarding multiple meta maps (Wait until Mahesh is a maintainer)
- Best Practices for multiple input:
- cf https://github.com/nf-core/modules/issues/4311
- Refactoring blog post (Sateesh)
- cf https://hackmd.io/@nf-core/SyD9jNbE6
- New Nextflow version not mounting $HOME:
- [Problem with `check_samplesheet.py`](https://github.com/nf-core/configs/pull/592/files#r1400299781)
- [Problem in one module, see slack thread](https://nfcore.slack.com/archives/CJRH30T6V/p1697729798874319)
- Should we set `NXF_SINGULARITY_HOME_MOUNT` in the template config?
- or deal with it within the singularity config scope
- Tests with differences between docker/singularity/conda (grrr bam files)
- Modules using meta.X

### Actions point

- Run tests for all modules in spring cleaning
- Be stricter about outcome/failures -> document
- Test all the modules script: https://github.com/grst/nf-core-test-modules
- Tools to handle the environment.yml
- Docs
- Coordinate, announce/document and TEST changes all at once
- Document the NXF_SINGULARITY_HOME_MOUNT issue: add https://nf-co.re/docs/usage/troubleshooting for now.
- Volunteers needed!
- Let's think about how to deal with bam/vcf files in nf-tests
- Plugins?
- Snapshot the filename
- Check if not empty
- Let's think about the snapshot files with nf-test and how to assess/read them
- Last 2023 meeting: december 15?
- common fields:
- meta fields
- params
- samplesheet fields
- emit/take || input/output fields
- Governance:
- what a maintainer is and entails too?
- Think about github teams and check what can a maintainer do
- Tests more in ops

## 2023-10-27

### Who

- @maxulysse
- @nvnieuwk
- @mashehu
- Jon manning

Focus is hackathon follow up: nf-test migration and refactoring pipelines.
@mashehu is leading the infrastructure front
@maxulysse is leading the pipeline refactoring front
@nvnieuwk and Jonathan Manning will be coordinating and managing the general effort and making sure we stay on target.

## 2023-09-22

### When/Where

https://zoom.us/j/93254682925?pwd=TW9GdU1YeU1EVnE2aFMvdDNkY2t1Zz09

### Who

- @maxulysse
- @FriederikeHanssen
- @nvnieuwk
- @sateeshperi
- @sppearce
- @emiller
- @jmir
- @mashehu
- @JoseEspinosa
- @christopher-mohr
- @anders sune

### Action Points from last time

- (Everyone) Give feedback for Rob on the guidlines conslidation
- (Ram) will update modules docs on genomic references ideally having meta next week
- (Rike) Will open a PR on PR etiquette docs --> Not done :sob:

### Agenda

- Hackathon
- Update: https://nf-co.re/events/2023/hackathon-october-2023/
- Project Board (urgent)
- Clean up your own repositories
- Tools release is coming
- Be ready for sync PRs
- Ideas for refactoring:
- https://github.com/nf-core/fetchngs/pull/188/files#diff-802c4789693708595d90ad84a76bbf834d6e070b07da42d4d72da8b48a2b58fc
- Heated discussion whether having multiple config files makes live easier. Points of concern:
- Difficult to figure out which config now would have which parameter, when a module is used multiple times with different parameters and ensure priority
- Patch on nextflow.config would make it super difficult to read
- Easier to deal with nf-test
-
- Contributing guidelines + Issue/PR templates
- Especially on nf-core/modules
- Come and ask for review on Slack
- Bring more subworkflows in nf-core/modules
- Which fields should we recommend in the meta map?
- Common params to be shared in between pipelines
- Common fields within the samplesheet
- Pipeline specific configs by default in TEMPLATE (cf: https://nextflow.slack.com/archives/C02TPTREJ03/p1689844381095889)
- Need to create a file in nf-core/configs for each pipeline
- Generally: any issues/problems/...?
- Module with diverging meta map names:
- Consensus: No. Was cleared up with the author
- How should we deal with multiple samplesheet options?
- Allow multipe different input parameters?
- Update nf-validation to handle conditional sample-sheets
-

### Action Points

## 2023-06-30

### When/Where

Zoom: https://eu01web.zoom.us/j/64977955782?pwd=YzRVRHArcGZ4MkN3NllZT2pRanhYQT09

### Who

@jfy133
@jasmezz
@nvnieuwk
@maxulysse
@jmir
@FriederikeHanssen
@JoseEspinosa
@louperelo
@mashehu

and

Rob
Daniel
Sofia
Ram
Matthias D
Sateesh
Edmund
(and whoever else I forgot)

### Agenda

- [ ] Action points from last time
- [x] guidance documentation consolidation (@robsyme)
- [PR is open](https://github.com/nf-core/nf-co.re/pull/1814)
- [x] nf-test 'community' adoption guinea pigs: test documenation/slides for 'self-' incorporation into their pipelines (Jon/Julia/Jose/Louisa)
- Overall going well, Sateesh will take a break now, as in a good 10 pipelines or so -> He will do a bytesize to open it to other developers to do it themselves (with a sample pipline example)
- Adding to template? For nf-core/tools 2.10 (implementation during hackathon)?
- [x] Volunteers to test nf-validation's Channel.fromSamplesheet() (@jmir & Rike/Sofia/Louisa)
- Tested/being in funcscan and sarek (some errors), but won't be in template until 2.10 (but you can ask Julia/Nicolas/Matthias if you want it earlier)
- [ ] meta for genomic references as general recommendation (Ram)
- Next week
- [x] Next meeting: discuss summer break
- (@jfy133) How is everything going? Overloaded/Underloaded? Feeling good or bad about anything?
- Anyone feeling uncomfortable in their role?
- Everything is fine! Always contact James/Rike/Maxime if you have any problems and want to report privately
- (@FriederiekeHanssen) Should we add guidelines on how to make a PR? (i.e. one feature per PR,... https://hugooodias.medium.com/the-anatomy-of-a-perfect-pull-request-567382bb6067
https://www.atlassian.com/blog/git/written-unwritten-guide-pull-requests
https://www.freecodecamp.org/news/git-best-practices-commits-and-code-reviews/)
- Rike to make a draft PR to get comments/feedback/agreement (and then maybe a new bytesize?)
- https://nf-co.re/events/2021/bytesize-4-github-contribution-basics Alex's bytesize with best pratice guidelines
- (@jfy133) Publication guidelines!
- Comments: https://github.com/nf-core/nf-co.re/pull/1811
- (@jfy133) hicar release review 😬
- Julia, Simon, Edmund, Jose
- Issue: people developing on fork! (e.g. HiC)

### Action Points

- (Everyone) Give feedback for Rob on the guidlines conslidation
- (Ram) will update modules docs on genomic references ideally having meta next week
- (Rike) Will open a PR on PR etiquette docs

## 2023-05-26

### When/Where

Gather! (probably or not...)

Zoom: https://eu01web.zoom.us/j/67778335655?pwd=MXQwaGZKT1JMeXFJTWdiWGRpQWVsQT09

### Who

@asp8200
@JoseEspinosa
@sateeshperi
@jfy133
@jmir
@ramprasadn
@nvnieuwk
@louperelo
@maxulysse
@pinin4fjords

### Agenda

- Last time
- @robsyme to update documentation structure to consolidate all guidelines files into one place
- Happening after _this_ meeting
- @sateesh to post in #pipeline-maintainers pinging main devs of nf-test PoC pipelines
- Added to fetchngs, methylseq, rnaseq, ampliseq
- Has to be done on a per-pipeline basis (can't do mass update) -> somewhat custom per pipeline
- Jose Question: minimum default requirements (assertions: version, test success etc.), then pipline dev can extend as they want?
- @mashehu and @jmir to #bytesize latest tools release
- Will wait until next release that has more cool stuff
- nf-validation & Channel.fromSamplesheet() @jmir
- To be added to next release
- Adding meta to genomic reference files
- Reminder to everyone: when reviewing please remind people to do this!
- It's becoming tricky with subworkflows
- General: How's being a maintainer going?!
- Comes in bursts
- Maxime will get us more swag ;)
- sc-flow discussion?
- They sound willing, nothing ever happens...
-

### Action Points

- nf-test 'community' adoption guinea pigs: test documenation/slides for 'self-' incorporation into their pipelines
- This time
- Jon: differntialabundance
- Jose: atacseq or chipseq
- Julia: crisprseq
- Next time:
- Louisa: funcscan
- ...
- Volunteers to test Channel.fromSamplesheet()
- Sarek: Rike
- Funcscan: Louisia
- Taxprofiler: Sofia
- meta for genomic references as general recommendation
- Ram to add to guidleines (if missing)
- Next meeting: discuss summer break

# nf-core/maintainers meeting

## Meeting 2023-04-28

### When/Where

2023-4-28 15:00-16:00 CEST, gather.town

### Who?
@mashehu , @jfy133 , @louperelo, @ramprasadn, @pinin4fjords, @jmir, @jasmezz, @robsyme, @christopher-mohr

### Agenda

- Review last meetings TODO
- ✅ @mashehu to update website to add all maintainer listed in last meeting
- PROMISES TO DO IT AFTER THIS MEETING
- - Need to update list of maintainers on website (during spring cleaning)
- ❌ Guidelines consolidation
- All under `Guidelines` folder
- Drop DSL2 prefix
- @robsyme to take stab
- PR here: https://github.com/nf-core/nf-co.re/pull/1814
- new tools release upcoming
- Today or next week
- Main changes:
- README restructure;
- container registry param (default quay, but can use own) - allows more flexible selection
- python 3.7 is dropped (as is nf-core/modules)
- JSON schema for meta.yml -> will be linted
- If time: review [orphaned questions](#orphaned-questions)
- General 'Custom' R/python etc. scripts in modules? Y/N?
- Issues: no versioning? QA of the custom (variable) language scripts more dificult? Would require a changelog etc.; Discoverability - when to know when reused (or should be reused thus pushed to a nf-core/module!)
- If used in more than one pipeline it should be moved from local to a custom module (@emiller will make an issue to try to collect these)
- Local modules keywords somehow? Then can periodically screen for popular custom modules/scripts that get copy-pasted to other pipelines and could propose to make a full module
- Difficult to find a definition of when should move from a pipeline-local to a full-module
- GUIDANCE: Ok if it's a one off, but if getting more and more used should move to separate package.
- So, e.g. if deseq/? grows more modules, the templated scripts should be pushed out to separate package??

- **nf-test** pipeline PRs for review:
- [fetchngs](https://github.com/nf-core/fetchngs/pull/151)
- [rnaseq](https://github.com/nf-core/rnaseq/pull/1020)
- [methylseq](https://github.com/nf-core/methylseq/pull/304)
- [demultiplex](https://github.com/nf-core/demultiplex/pull/104)
- [viralrecon](https://github.com/nf-core/viralrecon/pull/377)
- [ampliseq](https://github.com/nf-core/ampliseq/pull/580)
- [nascent](https://github.com/nf-core/nascent/pull/101)
- [viralintegration](https://github.com/nf-core/viralintegration/pull/43)

### Action Points

- @robsyme to update documentation structure to consolidate all guidelines files into one place
- @sateesh to post in #pipeline-maintainers pinging main devs of nf-test PoC pipelines
- @mashehu and @jmir to #bytesize latest tools release

## Meeting 2023-03-31

### When/Where

2023-03-31 15:00-16:00 CET , nf-core office gather.town

### Who?

### Agenda

Meeting was cancelled because everyone was hackathon-tired

## Meeting 2023-02-24

### When/Where

2023-02-24 15:00-16:00 CET , nf-core office gather.town

### Who?

@jfy133 @pinin4fjords @matthdsm @jmir @nvnieuwk, @mashehu, @louperelo, @ChrisHakk, @emiller

### Agenda

- ✅ Announcements
- ext.args/value channel meeting on 28 February 11:00-12:00 CET
- Review last meetings TODO (@jfy133)
- ❌ @mashehu to update website to add all maintainer listed in last meeting
- PROMISES TO DO IT AFTER THIS MEETING
- ✅ Rike to add a comment and pin about unrolling github previews on #request-review
- ✅ separate meeting to be had to hash out the two separate args issues (multi-tools, mandatory non-file inputs)
- ❌ Guidelines consolidation
- ✅ Review PR-to-master release [project board](https://github.com/orgs/nf-core/projects/39) (@jfy133)
- ✅ All ready for spring cleaning (@jfy133)?
- ✅ Should a `stub` section be required for new modules? (@matthdsm, @maxulysse)
- No 'nays' -> (Newbie?) hackathon task!
- ✅ JSON-schema for modules meta.yml [PR](https://github.com/nf-core/modules/pull/2913)
- General agreement good and to fail linting
- Deadline for review next Tuesday: https://github.com/nf-core/modules/pull/2913/files
- If time: review [orphaned questions](#orphaned-questions)
- General 'Custom' R/python etc. scripts in modules? Y/N?
- Issues: no versioning? QA of the custom (variable) language scripts more dificult? Would require a changelog etc.; Discoverability - when to know when reused (or should be reused thus pushed to a nf-core/module!)
- If used in more than one pipeline it should be moved from local to a custom module (@emiller will make an issue to try to collect these)
- Local modules keywords somehow? Then can periodically screen for popular custom modules/scripts that get copy-pasted to other pipelines and could propose to make a full module
- Difficult to find a definition of when should move from a pipeline-local to a full-module
- Need to update list of maintainers on website
- Keep a list of current plus previous maintainers
- Stickers
- If anyone has a concept for a hex design please send it to Chris and her will get some made
- ✅[Automated Conda lock file creation](https://nfcore.slack.com/archives/C043UU89KKQ/p1677146912693919) when modules are created, or conda settings updated?
- Jon to create feature request on tools repo

### TODO

- Issues for:
- Stub to module template https://github.com/nf-core/tools/issues/2192
- Conda lock file in tools

- Review slack channels during spring cleaning
## Meeting 2023-01-27

### When/Where

2023-01-27 15:00-16:00 CET , nf-core office gather.town

### Who?

@maxulysse, James, Jon, Jasmin, Matthias H, Louisa, Moritz, Nicolas, Gisela, Simon, Júlia, @emiller, Matthias dS, Rike, Daniel, Chris, Sofia

### TODO (for next time)

- @mashehu to update website to add all maintainer listed in last meeting
- Rike to add a comment and pin about unrolling github previews on #request-review
- separate meeting to be had to hash out the two separate args issues (multi-tools, mandatory non-file inputs)
- Standardise guidelines locations
- @jfy133 / @KuylkJ0AS0-limIJRUVsnw during spring cleaning?
- Or someone earlier?

### Agenda

- Review previous meeting TODO

- ✅ Rike:
- ✅ create poll for next meeting
- ✅ Write a message in request review about the new review emojis
- ❓Matthias H.: Add name/affiliation to website -> CAN DO NOW
- ✅ Everyone: add name/affiliation in list (in no particular order!)
- ⚔️ Maxime: Remove Github PR previews from Slack
- Can't do it, asking for another core member to help out
- Couldn't do it on a single channel, just use markdown instead
- ✅ Gisela: setup project board for PRs to `master`

- ✅ Review spring cleaning plan from Chris/James
- Add event to website (but don't advertise)
- Seperate meeting notes over here :point_right: [spring clean hackmd](https://hackmd.io/Hif6l9-wRMuY79uDuzEyiQ)

- ✅ nf-validate update from Júlia --> [meeting notes](https://hackmd.io/JEgfNwgYR2yo7zn6ouq_SA)

> :rotating_light: EMERGENCY TOPIC
> _Bring your tomatoes_ :tomato:
>
> - Should we allow 'named' ext.args? (`ext.args.<names>`) for mandatory non-file inputs OR require mandatory non-file `inputs:` channels
> - Should/how/where we document 'named' `ext.args`
>
> | args pros | args cons | val channels pros | val channel cons |
> |-----------|-----------|-------------------|------------------|
> | | | | |
>
>- Examples of modules/PRs/code that break/challenge the "rules"
- https://github.com/nf-core/modules/blob/master/modules/nf-core/controlfreec/freec/meta.yml
- https://github.com/nf-core/modules/blob/master/modules/nf-core/ascat/meta.yml
- https://github.com/nf-core/modules/pull/2648
- https://github.com/nf-core/modules/blob/master/modules/nf-core/untar/main.nf
> - Moving towards consensus but will need to organise another meeting to discuss this in greater detail with those who are interested
- @maxulysse, James, Jon, Matthias, Rike, Júlia, others?
- General consensus (- James' understanding): Basically: stick with file-only inputs/outputs, everything else goes via ext.args (no custom ones), with pipeline developers just needing to be familiar what they need for a tool to run when non-file mandatory parameters are required. Then we review the 'exceptions' in the list we have of modules that apparently required a deviation, and we assess why it was not possible to do thi sa t a pipeline level

- Guidelines locations
- Very scattered all over the place; makes it difficult for [maintainers to know what to follow](https://nfcore.slack.com/archives/C043UU89KKQ/p1669384160085619?thread_ts=1669381894.077609&cid=C043UU89KKQ)
- Can we standardise?

### Meeting Notes

- ❓Matthias H.: Add name/affiliation to website -> CAN DO NOW
- ⚔️ Maxime was voted down on remove Github repo previews from Slack
- Couldn't do it on a single channel which was the main issue (request-reviews), just use markdown instead (or manually close the preview)
- Everyone reminded to start adding release reviews to projets board
- Guidelines locations
- Matthias can look into adding check boxes
- James, Rike: Sort out markdown files during spring cleaning, but if someone beats us to it.... ;)
- Un-nf-corey pipelines (prompted by https://github.com/nf-core/viralintegration/pull/52)
- Consensus was a pre-v1.0.0 release
- Contributor must have record of standards-compliant contributions and promise to fix it up
- Pipeline will eventually get archived if that doen't happen

### TODOs

## Meeting 2022-11-25

### When?

Friday, 25 November⋅13:00 – 14:00 (CET), nf-core office gather.town

### Who?

Rike\*, James, @maxulysse, Matthias De Smet, Jon Manning (Healx Ltd, Cambridge), Nicolas, Daniel Straub (@d4straub)\*, Moritz Beber, Gisela Gabernet (@ggabernet)\*, Chris Mohr, Anders Jemt, Jose Espinosa-Carrasco, Louisa Perelo (@louperelo)\*, Ram, Harshil, Simon Pearce, Matthias Hörtenhuber, Anders Sune Pedersen (Danish National Genome Center), Matthieu Muffato (@muffato, Wellcome Sanger Institute)

\* Quantitative Biology Center (QBiC), Eberhard Karls Universität Tübingen, Germany

### TODOs (for next time):

- Rike:
- create poll for next meeting
- Write a message in request review about the new review emojis
- Matthias H.: Add name/affiliation to website
- Everyone:
- add name/affiliation here (in no particular order!)
1. Jose Espinosa-Carrasco ([Centre for Genomic Regulation](https://www.crg.eu/))
2. Jon Manning, ([Healx Ltd](https://healx.ai/))
3. Moritz E. Beber, ([Unseen Bio ApS](https://unseenbio.com))
4. James A. Fellows Yates ([Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute](https://www.leibniz-hki.de/en/) & [Max Planck Institute for Evolutionary Anthropology](https://www.eva.mpg.de/))
5. Maxime U. Garcia ([Seqera Labs](https://seqera.io))
6. Nicolas Vannieuwkerke ([Center For Medical Genetics Ghent](https://www.cmgg.be/en/))
7. Matthias De Smet ([Center For Medical Genetics Ghent](https://www.cmgg.be/en/))
8. Anders Sune Pedersen ([Danish National Genome Center](https://eng.ngc.dk/))
10. Anders Jemt ([Science for Life Laboratory](https://www.scilifelab.se/))
11. Ramprasad Neethiraj ([Science for Life Laboratory](https://www.scilifelab.se/))
12. Edmund Miller ([University of Texas at Dallas](https://biology.utdallas.edu/) & [Element Biosciences](https://www.elementbiosciences.com/))
13. Rob Syme ([Seqera Labs](https://seqera.io))
14. Jasmin Frangenberg ([Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute](https://www.leibniz-hki.de/en)
16. Adam Talbot ([Nonacus](https://nonacus.com/))
17. Simon Pearce ([Cancer Research UK Manchester Institute](https://www.cruk.manchester.ac.uk/))
18. Daniel Lundin ([Linnaeus University](https://lnu.se/))
19. Gisela Gabernet ([Quantitative Biology Center, QBiC, University of Tübingen](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/))
20. Friederike Hanssen ([Quantitative Biology Center, QBiC, University of Tübingen](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/))
21. Júlia Mir Pedrol ([Quantitative Biology Center, QBiC, University of Tübingen](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/))
22. Louisa Perelo ([Quantitative Biology Center, QBiC, University of Tübingen](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/))
23. Sofia Stamoul ([Karolinska Institute](https://ki.se) & [Karolinska University Hospital](https://www.karolinska.se/en/karolinska-university-hospital/))
24. Harshil Patel ([Seqera Labs](https://seqera.io))
- Dormant contributors
- Christopher Mohr ([Medical Data Integration Center Tübingen](https://www.medizin.uni-tuebingen.de/de/das-klinikum/einrichtungen/institute/informationstechnologie-und-medizininformatik/medic)) --> has switched positions (comment by Rike)
- Matthieu Muffato ([Wellcome Sanger Institute](https://www.sanger.ac.uk/))

- Ping Rike if you are not in the right teams (github, slack)
- Reserve week of 7th March for spring cleaning week!
- Maxime: Remove Github PR previews from Slack
- Can't do it, asking for another core member to help out
- Gisela: setup project board for PRs to `master`

### Agenda

#### General Topics

- Definition of roles/tasks
- Members: Generally quite active across different topics (modules,subworkflows,pipelines,....) --> Recognize this effort & formalise it
- Structure of group:
- Flat structure
- Chairs (number, who etc.: interim - Friederike, James, @maxulysse)?
- Assign responsible persons for specific tasks (e.g. test data clean up), decide at the time
- Suggested tasks:
- Review PRs
- Review release PRs (including first release)
- Module reviews
- Make sure the right people have access to the right repos (core)
- On-boarding people: check #github-invitations
- Clean up: e.g. Manage test data, stale PRs
- Update our own dockerhub hosted containers (`ensemblvep`, `snpeff`, `bclconvert`, `bcl2fastq`: @matthdsm + @maxulysse)
- push to dockerhub : @maxulysse
- Google calendars? or is this more an infrastructure or core tasks? (either way: @maxulysse)
- Contribution requirements
- From the core side: not a strict monitoring
- Minimum Hours/Maximum Hours: i.e. how to make bosses less scared:
- 1-2 hours week recommended but not strictly required. Breaks are also ok (e.g. sick, parental leave, vacation).
- Not own works, but helping others
- Joining maintainer meetings on regular basis
- Monitor slack channels: request-review, github-invitations, help, nostupidquestions
- What info to have on website (to formalise role):
- Names
- Affiliation
- TODO: In addition: update instutions.yml with logos: add PR https://nf-co.re/docs/usage/tutorials/institution
- How regular to meet?
- Monthly meetings -> TODO: find a date/time
- Who presses 'merge'?
> [name=Edmund Miller] Emphasis on keeping that it's okay to not be perfect, stuffs going to break but we'll learn from it.
- Restrict merge rights to maintainers for common repositories. For pipeline merge rights stay open.
- Let people merge their own PRs
- Finalise @maintainers groups i.e., is everyone already in the groups etc! (slack/github etc.)
- Core team todo after meeting
- Please ping Rike if you are not in the slack group
- PRs reviews:
- Remove long github printing for the channel -> TODO Maxime
- Release PRs
- Often disappear in request-review channel and then don't get reviewed in time
- Review buddies?:
- How to include new people?
> [name= Friederike Hanssen] maybe not such an issue, as these are for more experienced people
- Collect release reviews on project board?
- Automate that e.g. with GitHub Actions workflows -> PR to add master can automatically be added to Project Board
- ~~Google sheet~~ --> Board view is spread sheet like enough
- Assign yoursefl to the PRs you review for tracking
- smaller PRs etc:
- :eyes: Looking at PR
- :checkmark: Approved PR
- :merge: Merged PR
> [name=James Fellows Yates] get github PR icons as emojis?
> [name=Mashehu] already there

#### Spring Cleaning!

Organised by: James & Chris Hakkaart

When:
- week of 07th of March 2023, before the hackathon
- Kick-off meeting on the monday, distribute tasks, form smaller groups
- Spread throughout the week as time permits
- Closing meeting on Friday

Idea:

Lots of old issues, PRs, test data etc. that we need to clean up once a year as maintainers.

**What should we do?**

- Archive old pipelines?
- Close stale PRs on nf-core/modules:
- For common repos: modules, test-data, PRs sometimes stay open for a long time
- Close stale issues on nf-core/modules
> [name=Edmund Miller] Stale issue bots that close the issues are bothersome, but something to tag them stale might be nice.
- For pipelines possibly not an issues
- Standardise existing modules/subworkflows metadata tags
- Clean up test data
- Add meta.ymls to test data for the modules repository
> [name=James Fellows Yates] this sounds like development rather than spring cleaning...?
- Check if all installed modules are actually used inside each pipeline :zombie:
> [name=Friederike Hanssen] this sounds like something that could be supported with linting...
- Remove anything linking to DSL1, it won't be supported anymore
- Go through docs and check they are up-to-date
- Remove existing groups on github/slack
- NEW: cleanup/standardise old subworkflows against updated guidelines
- NEW: S3 file cleanup (deleting old work dirs etc.)
- NEW: Clean up instution contacts on the website

#### Post-hackathon events:

- Possibly second event after hackathon
- To deal with time commitment: split into two groups, one before, one after

#### Topics to discuss in the upcoming months

- General 'Custom' R/python etc. scripts in modules? Y/N?
- Seeds in modules - leave to pipeline developer or enforce at module level
- https://nfcore.slack.com/archives/CJRH30T6V/p1669191026178369
- Specifications for a groovy-native samplesheet checking (separate meeting)
- Current requests:
- Order agnostic (don't care where, just have to be present)
- Check _across_ columns
- Allow additional columns (that get ignored)
> [name=Friederike Hanssen] Quite some work has been done on this in the past, would be good to collect that info/difficulties there first (I think Phil was pretty involved there, I think slack channel #sample-sheet)
- Guidelines as to what warrants/constitutes a workflow
- minimum number of tools?
- application?
- ...
- How to test using `nf-test`
- Specific requirements for modules, subworkflows, pipelines (workflow succes, md5sums, trace size...)
> [name=Edmund Miller] Should be a badge of honor they're employing a nf-core maintainer, like Microsoft employing Guido
> [name=Friederike Hanssen] This would make for a good bytesize talk
- remaining DSL1 pipelines need to be converted soon

## Orphaned Qs

If still relevent

- Breaking changes in nf-core/modules (e.g. directory structure, conda definition)
- Versioning modules guidelines?
- Seeds in modules - leave to pipeline developer or enforce at module level?
- https://nfcore.slack.com/archives/CJRH30T6V/p1669191026178369