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Hackathon March 2021

Documentation

The Documentation group will focus on working on documentation during the hackathon. This involves not only documentation of individual pipelines, but also documentation of:

Of course you're very welcome to work on any of the above (and share ideas on what you are missing currently?! - always happy especially of new people joining and helping out on anything). We have added a couple of points to our project board that you can assign yourself on if you want to. Please never hesitate to ask in our Slack channel here especially if things are unclear and you need a comment / opinion!

Tiny PRs with individual fixes are very welcome too, if you don't feel like making a large contribution (yet

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).

Primary focus

  1. Convert parameter docs to JSON schema for various pipelines
  2. Improve nf-core/config docs
  3. Add tutorial how to set up institutional configs? (James)
  4. Other documentation topics, e.g:
    a. DSLv2 tutorial for adding new modules (Francesco L?)
    b. …?

Group members

  • James Fellows Yates
  • Alex Peltzer
  • Francesco Lescai
  • Johannes Alneberg
  • Hanka Medova
  • Tuur M
  • Sangram
  • Renuka Kudva
  • Jun-Hoe Lee
  • Ramón Rivera
  • Anandashankar Anil

Param docs to JSON Schema - Achievements

Monday

  • [Alex] Updated nf-core/hlatyping

Tuesday

  • [Sangram] Updated nf-core/scrnaseq

Wednesday

  • [Tuur] Methylseq JSON schema (but was already done)

nf-core/configs docs - Achievements

Monday

Tuesday

Wednesday

Tutorials - Achievements

Monday

  • [James] Added new Tutorials sections of nf-core website under usage/developers

Tuesday

  • [James] Started work on a step-by-step tutorial how to write an institutional profile
  • [Hanka] worked on tutorial for adding institutions to nf-core

Wednesday

  • [Hanka] Finished tutorial for adding institutions to nf-core
  • [Francesco] Working on DSL2 modules tutorial, with the fgbio/fastqtobam example. Still work in progress.

Bytesize Transcription

Monday

  • [Renuka / Jun-Hoe Lee / Johannes Alneberg]: Started working on transcribing the nf-core/bytesize talks
  • [Renuka / Jun-Hoe Lee / Johannes Alneberg]: Fairly time consuming, prioritizing accessibility and readability.

Tuesday

Wednesday

  • [Johannes Alneberg]: PR merged for the 2nd transcript. Would be nice with links to the embedded video, issue created.
  • [Renuka Kudva]: Finished 3rd transcript and merged!
  • [Renuka Kudva]: Finished 4th transcript and merged!
  • [Renuka Kudva]: Started transcribing 6a.
  • [Jun-Hoe Lee]: Finished 1st transcript (merged). Started on 6b transcript
  • [Anandashankar Anil]: Three-fourths of the way through transcribing the 5th transcript.

Additional - Achievements

Monday

  • [Hanka]: Added some docs for Singularity

Tuesday

  • [Hanka]: There is never enough explanation in the docs. Few paragraphs added there.
  • [Ramón]: Added -profile info to the Pipeline Configuration page and the preferential usage of containers. Issue #303

Wednesday

  • [James]: Updated template sync docs on website with new branching procedure
  • [James]: More updates to template sync docs on website with new branching procedure
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