🚀 Training Documentation 🚀

16th-18th March 2022

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

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

• Section for pytest in Gitpod
• Issue 1055
• [PR #1089]https://github.com/nf-core/nf-co.re/pull/1089
• Needs review

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

• Nextflow cheatsheet in Markdown summarizing processes, workflows, and functions
• Issue 1084
• Currently, a collaborative document on HackMD.io: https://hackmd.io/NBtD0prcTIa9szfJU7Do7Q?both

Day 2

• Issue 1084

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

• issue 1099 Paul C