<!-- .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/hEDjpCs.png" width="65%"><img></a> # 🚀 Training Documentation 🚀 _16th-18th March 2022_ <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 --- # 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](https://github.com/nf-core/nf-co.re/issues/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](https://github.com/carpentries-incubator/workflows-nextflow/issues/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](https://github.com/nf-core/nf-co.re/issues/637) now closed! --- # nf-core tutorial * Split into usage tutorial and contributor tutorial [name= 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](https://github.com/nf-core/nf-co.re/issues/1084) * Currently, a collaborative document on HackMD.io: https://hackmd.io/NBtD0prcTIa9szfJU7Do7Q?both --- Day 2 * [Issue 1084](https://github.com/nf-core/nf-co.re/issues/1084) --- Day 3 * Restructured the cheatsheet to make the sections clearer * Added the cheatsheet to GitHub. It can be found here : [Nextflow cheatsheet](https://github.com/chlazaris/Nextflow_training/blob/main/nextflow_cheatsheet.md) --- # Improve troubleshooting documentation @alxndrdiaz * Added ed new section explaining basic troubleshooting steps. * [Issue 1081](https://github.com/nf-core/nf-co.re/issues/1081) --- # Add Guide to create training materials. @mahesh-panchal * Add a guide on how to contribute training material to a common framework. * [Issue 1056](https://github.com/nf-core/nf-co.re/issues/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](https://github.com/nf-core/nf-co.re/issues/698) --- # Add simple example to build R container with R packages * [issue 1099](https://github.com/nf-core/nf-co.re/issues/1099) [name= Paul C]