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Welcome to the NF_workshop wiki!

Agenda

• Day 1 - Tuesday, January 23
• Day 2 - Wednesday, January 24
• Day 3 - Thursday, January 25

Before the workshop begins, please check out:

Set up UT linux account and environment

Data used in this course:

We'll be using a practice RNA-Seq dataset from the Griffith Lab. If you would like to practice on an alternative small dataset consisting of fastq files, you are welcome to do so.

To Download the data, in your personal UTK0262 NF_workshop directory, navigate to raw_data/fastq_seqs. Run the get_fastq_seqs.sh script to start downloading the raw fastq reads. Likewise, the raw_data/refs directory contains the script get_refs.sh to download the reference chromosome and annotation (gtf) file.

Other useful resources:

Nextflow:

• Nextflow recommended training materials
• Software Carpentries Nextflow Lessons (in development)
• Nextflow Slack Channel
• NF-core

Containers:

• Moreau et al 2023 Containers for computational reproducibility
• BioContainers recipes

Upcoming workshops of interest:

• Orientation to ISAAC-NG (Jan 26)
• Git: A lab notebook for your computational work (Feb 2)