/nfcoreWorkshopTesting

testing and materials development for AusBioCommons customising nf-core workshop 2023

Primary LanguageShell

nfcoreWorkshopTesting

Testing and materials development for AusBioCommons customising nf-core workshop 2023.

Materials developed by:

  • Cali Willet
  • Chris Hakkaart
  • Georgie Samaha

How this repo works

This repository contains draft materials and details regarding their development for the Australian BioCommons customising nf-core workshop. Materials have been organised into separate directories for parts 1 and 2:

  • Create a subdirectory for each exercise or session to be run in each part
  • See Materials testing for instructions on what information to provide for each session/exercise
  • Include any useful files and scripts for each exercise/session in the relevant subdirectory
  • See Download materials for how to get workshop data
  • See Issues and troubleshooting for nf-core GitHub issue template

Set up Nimbus environment

Instances set up using Nimbus bioimage which has Singularity, Nextflow, Docker already installed.

NOTE: See NIMBUSSETUP.md for instructions on setting up your test instance.

Download rnaseq pipeline

Download and install nf-core/rnaseq code with:

git clone https://github.com/nf-core/rnaseq.git

Download materials

Using the same dataset as rnaseq workshop, but needed to recreate STAR indexes for most recent stable release of nf-core/rnaseq workflow and opting to rename files and directory for sake of clarity. Will send updated materials to Alex to be uploaded to cvmfs once finalised. For now materials are on Cloudstor (and subject to change) and contain:

  • mm10_reference/mm10_chr18.fa
  • mm10_reference/mm10_chr18.gtf
  • mm10_reference/STAR/ (star index files)
  • samplesheet.csv (check path to fqs: /home/ubuntu/nfcoreWorkshopTesting/materials/)
  • fastqs/
  • README.md

Download subset/test data from Cloudstor

wget -O nfcore_materials.tar.gz https://cloudstor.aarnet.edu.au/plus/s/gIBdDhKEwfq2j58/download

Unpack the files:

tar -zxvf nfcore_materials.tar.gz

Materials testing

Notes for each exercise draft have been included in the Part1 and Part2 directories. In each exercise/part README.md, include:

  • Objectives
  • Testing reflection
  • Content draft
  • Troubleshooting
  • Links/resources

A template README.md can be found at: nfcoreWorkshopTesting/exerciseREADME.md

Issues and troubleshooting

Any issues with nf-core/rnaseq workflow needs to be submitted as an issue on their GitHub page and shared with Chris Hakkaart. A template for submitting bugs is here. Please link to all issues below: