---
title: Infrastructure Team - nf-core Hackathon March 2023
tags: march-2023,nf-core,hackathon,progress
description: View the slide with "Slide Mode".
---

<!-- .slide: data-background="https://raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg" -->

<a href="https://www.nf-co.re"><img src="https://i.imgur.com/FsQmcYZ.png" width="65%"><img></a>

### 🚀 Infrastructure Team 🚀

_27th-29th March 2023_

The Hackathon March 2023 [Project Board](https://github.com/orgs/nf-core/projects/41)
The Group Discussion Channel `#hackathon-march-2023-infrastructure`

<img src="https://openmoji.org/data/color/svg/E040.svg" width=50> @nf-core / <img src="https://openmoji.org/data/color/svg/E045.svg" width=50> @nf-core

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# Infrastructure Team

- Leads
- @mirpedrol
- @mashehu

---

# General development work

:hammer_and_wrench: nf-core/tools subworkflow functionality
:heavy_check_mark: improve nf-core/tools test coverage
:dark_sunglasses: Rewrite nf-co.re with astro
:bug: Bug fixes for nf-co.re

---

# Remember

- Add yourself to Team Members slide
- Assign yourself on issues on the [project board](https://github.com/orgs/nf-core/projects/38/views/11)
- Post your progress here **daily**!
- Sign up for a reviewing buddy (see slide)!

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# Team Members

<small>

- Júlia Mir Pedrol (@mirpedrol)
- Matthias Hörtenhuber (@mashehu)
- Anne Marie Noronha (@anoronh4)
- Adrien Coulier (@Aratz)
- Sofia Haglund (@sofiahag)
- Arthur Gymer (@awgymer)
- Karthik Nair (@KarNair)
- Novak Martinovic (@NovakApis)
- Dubravka Jevtic (@Djevtic-Persida)
- Fabian Egli (@fabianegli)
- Ash Holland (@sersorrel)
- Maxime Garcia (@maxulysse)
- Nikola Jurasović (@JuraNJ)
- Harshil Patel (@drpatelh)
- Rob Syme (@robsyme)
- Adam Talbot (@adamrtalbot)
- Esha Joshi (@ejseqera)
- Hatem Nawar (@hnawar)

</small>

---

# Day One

<small>

- Sofia, Sort and mark issues as done on the GitHub project page:
- [#1265](https://github.com/nf-core/tools/issues/1265) "Edit this page on github button not working" - [PR](https://github.com/nf-core/nf-co.re/pull/1684)
- [#1154](https://github.com/nf-core/tools/issues/1154) "Reorganise the different tutorial links" - [PR](https://github.com/nf-core/nf-co.re/pull/1688)
- Arthur:
- [#2143](https://github.com/nf-core/tools/issues/2143) "Dump custom template yml when creating pipeline" [[MR #2189](https://github.com/nf-core/tools/pull/2189)]
- [#1840](https://github.com/nf-core/tools/issues/1840) "Don't use `System.exit(1)`" [[MR #2211](https://github.com/nf-core/tools/pull/2211)]
- Adrien - [#1895](https://github.com/nf-core/tools/issues/1895) "Implement tests for `nf-core subworkflows create-test-yml` command"
- Karthik - [#1466](https://github.com/nf-core/tools/issues/1466) tag gitpod docker images by branch"
- Novak - [#2200](https://github.com/orgs/nf-core/projects/38/views/11?filterQuery=type&pane=issue&itemId=23475153) "Convert nf-core/tools to typed python"
- Dubravka - [#1283](https://github.com/nf-core/nf-co.re/issues/1283) "Broken/missing links for contributing guidelines" issue closed
- Fabian - [#1796](https://github.com/nf-core/tools/issues/1796) Deprecate Python 3.7 for nf-core tools
- Ash: [#2212](https://github.com/nf-core/tools/issues/2212) found a (probable) bug in handling of deprecated `.nf-core-lint.yaml`
- Anne Marie: [#2213](https://github.com/nf-core/tools/pull/2213) Additional linting for deprecated `params.enable_conda`

</small>

---

# Day Two

<small>

- Sofia:
- [#1648](https://github.com/nf-core/tools/issues/1648) "Parameters: make fa icon heading link" - [PR](https://github.com/nf-core/nf-co.re/pull/1713)
- Arthur
- [#1920](https://github.com/nf-core/tools/issues/1920) "Add functionality to remove patches" [[MR #2216](https://github.com/nf-core/tools/pull/2216)]
- [#1840](https://github.com/nf-core/tools/issues/1840) "Don't use `System.exit(1)`" [[MR #2211](https://github.com/nf-core/tools/pull/2211)]
- Maxime:
- [#3170](https://github.com/nf-core/modules/pull/3170) - Grouped all `mus_musculus` sub keys in the same map in the `test_data.config` file
- Adrien
- [#1895](https://github.com/nf-core/tools/issues/1895) "Implement tests for `nf-core subworkflows create-test-yml` command"
- Novak
- [#2200](https://github.com/orgs/nf-core/projects/38/views/11?filterQuery=type&pane=issue&itemId=23475153) "Convert nf-core/tools to typed python" (still tackling)
- 🐤🏆QUIZ WINNER 🏆🐤
- Karthik:
- [#1841](https://github.com/nf-core/tools/issues/1841) nf-core schema build changes default value from null to "None"
- Edmund Miller:
- [#2165](https://github.com/nf-core/tools/pull/2165) Replace requests_mock with responses

</small>

---

- Fabian:
- Implementing fixtures to speed up pytests.
- Anne Marie:
- [#2213](https://github.com/nf-core/tools/pull/2213) Add lint tests finding deprecated params.enable_conda
- Matthias & Júlia:
- Use gitpod dev container in tools dev branch

---

# Day Three

<small>

- Sofia:
- [#1648](https://github.com/nf-core/tools/issues/1648) "Parameters: make fa icon heading link" - [PR](https://github.com/nf-core/nf-co.re/pull/1713)
- [#1445](https://github.com/nf-core/nf-co.re/issues/1445) "Error 404". The incorrect link is for an old release. Not sure where the links are fetched from?
- [#1357](https://github.com/nf-core/nf-co.re/issues/1357) "Change the styling/location of the Edit button for pages". Maybe just change the opacity to 1? - [PR](https://github.com/nf-core/nf-co.re/pull/1731)
- [#1058](https://github.com/nf-core/nf-co.re/issues/1058) "broken header links with code headings". Same here, not sure where the links are fetched from.
- Nikola:
- [#1028](https://github.com/nf-core/nf-co.re/issues/1028) - Working on adding module usage examples on module pages on nf-co.re (astro)
- Adrien
- [#1895](https://github.com/nf-core/tools/issues/1895) "Implement tests for `nf-core subworkflows create-test-yml` command"
- Ash
- [#2221](https://github.com/nf-core/tools/pull/2221) "Make `nf-core modules lint` use new config file"
- [#2225](https://github.com/nf-core/tools/pull/2225) "Don't require an argument for `nf-core schema lint`"

- Arthur
- [#2205](https://github.com/nf-core/tools/issues/2205) "Linting process labels with multiple underscores fails" General improvements to label linting [[MR #2227](https://github.com/nf-core/tools/pull/2227)]

</small>

---

<small>

- Matthias:
- [#2190](https://github.com/nf-core/tools/pull/2190) Made some progress on: add schema based validation for meta.ymls to linting
- Karthik:
- [#1841](https://github.com/nf-core/tools/issues/1841) nf-core schema build changes default value from null to "None"
- Fabian:
- [2226](https://github.com/nf-core/tools/pull/2226) Use more pytest fixtures in modules tests (for faster test)
- Hatem:
- [481](https://github.com/nf-core/configs/pull/481) New profiles for google

</small>

---

<small>

- James:
- [#1728](https://github.com/nf-core/nf-co.re/pull/1728) Docs for Harshil alignment(TM)

</small>

---

# Automated multi-cloud testing!
## :cloud::rocket:

Contributors: Adam / Esha / Harshil / Rob

---

<small>

- GCP (Esha)
- Smash GCP credits provided for Hackathon!
- Create Compute Environment in nf-core megatests account
- Test `-profile test`, `-profile test_full` nf-core/rnaseq
- Test `-profile test`, `-profile test_full`, `-profile test_full_nanopore` nf-core/viralrecon
- Test `-profile test`, `-profile test_full` (:hourglass:) nf-core/sarek

</small>

---

<small>

- Azure (Adam)
- Finally set-up nf-core Azure account - compute and storage
- Create Compute Environment in nf-core megatests account
- Cloned igenomes human data to nf-core Azure storage
- Test `-profile test` and `-profile test_full` nf-core/rnaseq

</small>

---

<small>

- Github Actions (Rob / Harshil)
- Re-write existing AWS CI for small and full sized tests for nf-core/rnaseq
- Add `workflow_dispatch` logic to choose cloud provider
- Add and standardise Github `secrets` for use with Actions
- Test and include new Tower Actions (moved to `seqeralabs/action-tower-launch`)
- Push pipeline notifications to new Slack #megatests-alerts channel
- Add custom runner on Azure so we could finish! (Adam)

</small>

---


---

# Summary

17 Team Members
- Tools
37 PRs merged
27 Issues closed
- nf-co.re
8 PRs merged
3 Issues closed

---

Achievements
- One of our team members won the Quiz! :first_place_medal:
- We broke GitHub! :smile_cat:
- We broke Kahoot! :question:
- Tests weren't running! :running: