# 2025 spring cleaning

## The MAIN plan

### nf-core/modules

Leads: Famke, Simon, Mahesh, **Florian**

- [BOARD PRs](https://github.com/orgs/nf-core/projects/97)
- [BOARD Issues](https://github.com/orgs/nf-core/projects/102)
- Stale branches
- Stale PRs
- PRs:
- Bumped PRs: 51
- Closed PRs: 62
- Needs help: 10
- Stay open: 19
- In progress: 25
- Issues:
- To do: 192
- Bumped: 66
- Closed: 72
- In Progress: 49
- Suggestion: 26
- No status update yet: 143 (too many issues for our small but mighty team)
- :rocket: Special shoutout to Famke for being MVP and dealing with 53 PRs and 108 issues!!! :rocket:
- Suggestion for next spring cleaning: Setup boards at beginning with `gh cli` as they were extremely helpful
- Standardise metadata tags formatting
- Clean up old subworkflows to match current guidelines
- Flag modules with custom meta fields
- params usage
- Action item: Update opening issues to tag with types for bug when issuing bug report, rather than just labels (in general use types more going forward)

### nf-core/pipelines

Leads: Lorena, **Jonas**, Nico T, Jon, Jose

- [BOARD](https://github.com/orgs/nf-core/projects/98)
- [Check pipeline health page](https://nf-co.re/pipeline_health)
- Check tags: all pipeline should have useful tags (whatever that means…)
- Check all nf-core pipelines are on nf-co.re
- Maybe it is check if nf-core is the main
- Check that AWS tests passed for released pipelines
- Stale issues(?)
- Stale branches
- Stale PRs
- Label pipelines that are very behind in templates to make a action plat to resurrect them?
- If pipelines seem not to be maintained actively, ping Slack channel, ping former maintainer(s), discuss action plan
- Following guidelines?

Backup: Specific pipelines
- Branches?
- Issues
- PRs
- Clean up project boards

### nf-core/documentation

Leads: **Matthias H**

- Reviewing for DSL1 reference (e.g., tutorials)
- Update references to latest version of Nextflow(?)
- Reference old Nextflow version for DSL1
- Checking tutorials works (installation, development etc.)
- Update links to Nextflow trainings
- or remove
- Check troubleshooting

### nf-core/configs

Leads: Maxime, **Joon**

- [BOARD](https://github.com/orgs/nf-core/projects/100/views/1)
- Stale issues: :white_check_mark:
- Closed: 4
- Waiting for update: 9
- Stale branches:
- Deleted 17 branches :fire:
- Stale PRs:
- Waiting for update: 10
- 5 merged
- 2 closed

### nf-core/test-dataset

Leads: **Maxime**, Simon

- [BOARD](https://github.com/orgs/nf-core/projects/100/views/2)

### Hackathon preparation

Leads: **Nicolas**, Júlia, Jose, Lorena

- [BOARD](https://github.com/orgs/nf-core/projects/99)
- Prepare project board (tools, documentation…)
- Move in some issues and add some tasks

### Core Team

Leads: James, Rike, **Maxime**, Jose, Edmund, Júlia, Nicolas, Matthias H, Fran

- [BOARD](https://github.com/orgs/nf-core/projects/96)

- Cleaning up slack/github groups/teams (Nicolas)
- Slack - not done ❌
- Github groups - UPDATED ✅
- Core team checklist - UPDATED ✅
- Clean up old/stale slack channels (Maxime)
- Most public channels investigated
- 3 closed
- 1 renamed
- 1 in waiting
- 15 are Maxime's stuff
- 1 was Matthias H
- Maintainers lead tasks (James, Rike, Maxime)
- Inactive members contacted ▶️
- New invitations to new one ▶️
- Updating website with maintainers info (See above) ❌
- Clean up pipeline proposal board (James)
- ~100 slack threads/repos reviewed ✅
- 37 proposals 'timed out' ✅
- 16 pipelines flagged for archiving by Maxime ✅
- Clean up special interest group proposal board (Jose)
- All live now ✅
- Archiving pipelines (Maxime)
- genomeskim
- Will go through the list from the pipeline.
- Merchandise (Fran)
- Ensure all custom logos represented on the webshop
- AWS account/AWS megatests (Rike, Jose) :arrow_forward:
- Check all pipelines have megatests
- Clean up CEs
- Clean up AWS account
- Check all non pipeline repos (Maxime)
- All 28 non pipeline repos investigated:
- Point of actions:
- https://github.com/nf-core/.github
- Should we add a member page?
- My guess is that all is covered or should be by website
- https://github.com/nf-core/basic_training :white_check_mark:
- Leave as is for now, we will see with Nextflow training team how to migrate and unify content
- https://github.com/nf-core/gh-actions-lint
- To archive?
- https://github.com/nf-core/hackathon
- To pipeline?
- https://github.com/nf-core/ops :question:
- https://github.com/nf-core/prettier-plugin-nextflow
- To archive?
- https://github.com/nf-core/stats
- Better README?
- https://github.com/nf-core/vale :question:

- NEXT YEAR: [review activity of interest groups](https://nf-co.re/blog/2024/special_interest_groups#closing-after-inactivity) (archive if nothing)

## nf-core/tools

Lead: **Júlia**

- deleted 34/55 branches (55->21)
- closed 8 PRs
- closed 29 issues (3 from 2020 2 from 2021!)

## Opening meeting

We agreed on the plan and we kickstarted it all

## Closing meeting

Attended:

- Maxime
- James
- Jose
- Famke
- Florian
- Jonas
- Rike
- Joon
- Julia
- Luisa
- Nicolas

Agenda:

- THANK YOU
- Each task force summarizes their progress
- nf-core/pipelines (Jonas)
- nf-core/modules (Florian)
- nf-core/documentation
- nf-core/configs
- nf-core/test-dataset
- Hackathon preparation
- Core Team (James)
- General feedback
- What went well?
- What can be improved?
- Tasks that should be more regular
- Update procedures and guidelines
- More regular cleaning
- THANK YOU

### Minutes / Points of discussions:

#### THANK YOU

- That was the BEST spring cleaning
- So many messages exchanged
- Shoutout to Famke for pinging James everyhere (@jfy133 :100:)

#### Pipelines:

- Stats
- 50 pipelines out of 116 were checked out
- 5 DSL1
- 8 not maintained
- 2/3 will not continue to be maintained
- Majority of pipelines was all good
- Couple of problems and issues were found, so issues were created for this
- James pestered every proposal that was not started
- Maxime will archive pipelines that needs archiving in a couple of weeks
- Discussions
- ⚒️ Need more people on pipelines team next time (quite large, domain-specific knowledge would help speed up) or 1 extra week
- ⚒️ We should push people to develop on nf-core
- A yearly check should be enough
- ⚒️ Last update of the dev branch should be featured on the pipeline health page

#### Modules:

- Stats
- PRs:
- Bumped PRs: 51
- Closed PRs: 62
- Needs help: 10
- Stay open: 19
- In progress: 25
- Issues:
- To do: 192
- Bumped: 66
- Closed: 72
- In Progress: 49
- Suggestion: 26
- Discussions
- Famke and Luisa are MVP (53 PRs reviewed by Famke, 108/106 Issues)
- Luisa DMed Maxime because he never check GitHub
- Everything tagged
- ⚒️ Prepare some boilerplate messages for posting on issues/PRs/channels
- We could have pre-saved messages even -> DUMP 2025 MESSAGES HERE: https://hackmd.io/OE_WueP2SD6XCeALyH-VUw
- Is 'new issue' thing really necessary
- Lots of 'junk' / abandoned
- Used as a wishlist
- ⚒️ We should automate tagging things prior spring cleaning?
- Be smarter with automatic replies / tags / types(!?)
- Replace tags with types
- Auto add stuff to hackathon boards?
- Let's continue yearly
- Additional stuff from Simon
- Standardise metadata tags formatting
- Clean up old subworkflows to match current guidelines
- Flag modules with custom meta fields
- params usage

#### Configs:

- Stats
- 11 Done
- 16 In progress
- Discussion
- Mostly Edmund
- ⚒️ Quite a few issues/PRs set up but the abandoned - this repo is not something we can test/someone can come and return - Stalebot
- ⚒️ Can we add a tag so stalebot ignore stuff that should not be closed?
- ⚒️ Tools will only have stalebot work if 'waiting feedback' tag

- Discussion:
- Regular cleanup is done more or less regularly by James and Maxime
- So there was less of an effort

#### Test-datasets

- No major activity (requires a bigger overhaul)
- James/Maxime wants to REDO it all

#### Hackathon preparation

- Ongoing - pestering people to add tasks to project board (300-400 issues)

#### Core team

- Stats
- Slack team update: no update
- Github groups: updated
- Core team checklist: updated
- Slack channels: most public investigated, 3 closed, 1 renamed, a few assigned to others
- Pipeline proposals: 100 checkeed, 37 proposals timed out, 16 flagged for archiving
- All accepted special interest groups now have websites (immunology, core facilities, other)
- Pipeline archiving: will do soon now has list from pipeline time/core
- AWS cleaning: checked all pipeliens have megatests, cleaning up CEs, cleaning up AWS account (will continue longer - needs core team discussion)
- Non-pipeline rpos:
- Discussion
- Can we link github team with slack teams to reduce manual
- >200 proposals (of all status), but hard to search
- ⚒️ Add keywords to proposals?
- ⚒️ Move from slack board to a github repository
- Lots of suggestions from Maxime
- ⚒️ https://github.com/nf-core/.github
- Should we add a member page?
- My guess is that all is covered or should be by website
-⚒️ https://github.com/nf-core/basic_training :white_check_mark:
- Leave as is for now, we will see with Nextflow training team how to migrate and unify content
- ⚒️ https://github.com/nf-core/gh-actions-lint
- To archive?
- ⚒️ https://github.com/nf-core/hackathon
- To pipeline?
- https://github.com/nf-core/ops :question:
- ⚒️ https://github.com/nf-core/prettier-plugin-nextflow
- To archive?
- ⚒️ https://github.com/nf-core/stats
- Better README?
- ⚒️ https://github.com/nf-core/testpipeline
- To pipeline?
- https://github.com/nf-core/vale :question:

#### tools

- Stats
- deleted 34/55 branches (55->21)
- closed 8 PRs
- closed 29 issues (3 from 2020 2 from 2021!)
- Discussion
- ⚒️ Should we auto-delete merged branches everywhere?

### General

- Modules: Simon very pro adding 'waiting feedback' stale bot system like in tools
- Modules: module requests should NOT be on modules, but should be on a pipeline - and linked back somewhere
- For wishlist modules -> a single issue with a list of requests, rather than one issue per
- Maybe auto close after 6 months if you don't plan to work on it?