Workshop to teach how to run nextflow pipelines
Learning Goals
After this workshops, students will be able to:
- Install nextflow
- Understand concept of workflow managers
- Run third-party or nf-core? Pipelines based on github readmes
- Evaluate quality/completeness of pipeline
- What does the pipeline do
- Figure out what are their config/parameter options
- How to make it run on the HPC
- How to run a workflow on the Cannon and O2 clusters
- Understand work directory vs publish directory
- Specify that the work directory goes to scratch
- Run a new workflow on small test data first
- How to read the logs and errors (nextflow log, workdir .command.err)
- Where to get help and how to ask (nextflow community, etc)
Pre-reqs
- Terminal, CLI, BASH
- Has previously run SBATCH jobs on the cluster
- Has previously run command line software before
- Does not have to have written any scripts themselves
- Has used conda or singularity in the past to manage software