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🚀 Training Documentation 🚀

16th-18th March 2022

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@nf-core /
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@nf-core


Team Members

  • Gisela Gabernet (@ggabernet)
  • Mahesh Binzer-Panchal (@mahesh-panchal)
  • Francesco Lescai (@lescai)
  • Francesca Miccolis
  • Jun-Hoe Lee
  • Umar Ahmad
  • Charalampos (Harris) Lazaris (@chlazaris)
  • John Arnn (@jwarnn)
  • Chris Hakkaart (@christopher-hakkaart)
  • Chris Wyatt (@chriswyatt1)
  • Saba Nafees (@snafees)
  • Alexander Ramos (@alxndrdiaz)
  • Dan Lu (@danrlu)
  • Erik Fasterius
  • Paul Cantalupo

Progress

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GitPod Docs

@chriswyatt1

  • Instructions for Gitpod in Developers/Using_gitpod_for_development
  • Section for Gitpod basics
  • Section for editing Markdown for nf-core webpage
  • Section for running a basic pipeline (rnaseq)
  • Basic information about the.gitpod.yml configuration
  • Section for git pull request

GitPod Docs


GitPod for Tutorials

@lescai - Day 1

  • Testing Gitpod (launch and env)
  • Conversation ongoing to choose use-case
  • Carpentries issue #68

Note: the issue in the hackathon project belongs to carpentries-incubator/workflows-nextflow


@lescai - Day 2

  • new nf-co.re branch for gitpod configs
  • nf_core_usage tutorial updated with gitpod button
  • this open gitpod env and automatically visualises tutorial on nf-co.re web page on top of a terminal
  • 2 PRs (tutorial #1094 + config branch #1093)

@lescai - Day 3

  • Ongoing conversation on how to best organise training materials (new repo? empty branch? open web page or code page?)
  • PRs #1094 and #1093 on hold waiting for Discord answer (can we pass parameters on URL to be used in config? most likely will be a "no")
  • reviewed Ed's PR #1090

Docs. local version of iGenomes

@christopher-hakkaart

  • Updated troubleshooting documentation
  • Updated reference genomes documentation
  • Issue 637 now closed!

nf-core tutorial

  • Split into usage tutorial and contributor tutorial GG
  • Updated usage tutorial to latest nf-core tools versions and slides

@WackerO tested and added some suggestions
@Hanka medová tested and added suggestions


NXF cheatsheet

@chlazaris @snafees @danrlu

Day 1


Day 2


Day 3

  • Restructured the cheatsheet to make the sections clearer
  • Added the cheatsheet to GitHub. It can be found here : Nextflow cheatsheet

Improve troubleshooting documentation

@alxndrdiaz

  • Added ed new section explaining basic troubleshooting steps.
  • Issue 1081

Add Guide to create training materials.

@mahesh-panchal

  • Add a guide on how to contribute training material to a common framework.
  • Issue 1056

Add guide for how to contribute to exisiting repo

@christopher-hakkaart

  • Add guide for how to best contribute to exisiting repo.
  • Weave in other relevant tutorials and documentation.
  • Issue 698

Add simple example to build R container with R packages

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