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🚀 Infrastructure Team 🚀

27th-29th March 2023

The Hackathon March 2023 Project Board
The Group Discussion Channel #hackathon-march-2023-infrastructure

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@nf-core /
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@nf-core

Infrastructure Team

  • Leads
    • @mirpedrol
    • @mashehu

General development work

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nf-core/tools subworkflow functionality
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improve nf-core/tools test coverage
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Rewrite nf-co.re with astro
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Bug fixes for nf-co.re

Remember

  • Add yourself to Team Members slide
  • Assign yourself on issues on the project board
  • Post your progress here daily!
  • Sign up for a reviewing buddy (see slide)!

Team Members

  • 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)

Day One

  • Sofia, Sort and mark issues as done on the GitHub project page:
    • #1265 "Edit this page on github button not working" - PR
    • #1154 "Reorganise the different tutorial links" - PR
  • Arthur:
  • Adrien - #1895 "Implement tests for nf-core subworkflows create-test-yml command"
  • Karthik - #1466 tag gitpod docker images by branch"
  • Novak - #2200 "Convert nf-core/tools to typed python"
  • Dubravka - #1283 "Broken/missing links for contributing guidelines" issue closed
  • Fabian - #1796 Deprecate Python 3.7 for nf-core tools
  • Ash: #2212 found a (probable) bug in handling of deprecated .nf-core-lint.yaml
  • Anne Marie: #2213 Additional linting for deprecated params.enable_conda

Day Two

  • Sofia:
    • #1648 "Parameters: make fa icon heading link" - PR
  • Arthur
  • Maxime:
    • #3170 - Grouped all mus_musculus sub keys in the same map in the test_data.config file
  • Adrien
    • #1895 "Implement tests for nf-core subworkflows create-test-yml command"
  • Novak
    • #2200 "Convert nf-core/tools to typed python" (still tackling)
    • 🐤🏆QUIZ WINNER 🏆🐤
  • Karthik:
    • #1841 nf-core schema build changes default value from null to "None"
  • Edmund Miller:
    • #2165 Replace requests_mock with responses
  • Fabian:
    • Implementing fixtures to speed up pytests.
  • Anne Marie:
    • #2213 Add lint tests finding deprecated params.enable_conda
  • Matthias & Júlia:
    • Use gitpod dev container in tools dev branch

Day Three

  • Sofia:

    • #1648 "Parameters: make fa icon heading link" - PR
    • #1445 "Error 404". The incorrect link is for an old release. Not sure where the links are fetched from?
    • #1357 "Change the styling/location of the Edit button for pages". Maybe just change the opacity to 1? - PR
    • #1058 "broken header links with code headings". Same here, not sure where the links are fetched from.

  • Nikola:

    • #1028 - Working on adding module usage examples on module pages on nf-co.re (astro)

  • Adrien

    • #1895 "Implement tests for nf-core subworkflows create-test-yml command"

  • Ash

    • #2221 "Make nf-core modules lint use new config file"
    • #2225 "Don't require an argument for nf-core schema lint"

  • Arthur

    • #2205 "Linting process labels with multiple underscores fails" General improvements to label linting [MR #2227]
  • Matthias:
    • #2190 Made some progress on: add schema based validation for meta.ymls to linting
  • Karthik:
    • #1841 nf-core schema build changes default value from null to "None"
  • Fabian:
    • 2226 Use more pytest fixtures in modules tests (for faster test)
  • Hatem:
    • 481 New profiles for google
  • James:
    • #1728 Docs for Harshil alignment™

Automated multi-cloud testing!

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Contributors: Adam / Esha / Harshil / Rob

  • 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 (
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      ) nf-core/sarek
  • 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
  • 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)

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!
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  • We broke GitHub!
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  • We broke Kahoot!
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  • Tests weren't running!
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