Running a NextFlow pipeline from nf-core

[wong-nw]

Start logging steps and taking notes to set up an nf-core pipeline run

[wong-nw]

1. Find a pipeline of interest from https://nf-co.re
2. Navigate to the usage page to determine necessary input files
3. Log on to biowulf and set up an interactive session
4. Set up the singularity cache to use the user's data directory instead of home (https://ccbr.github.io/HowTos/docs/containers/singularity-biowulf.html#cache-directory)
5. module load singularity and module load nextflow
6. Test the workflow with built in tests
   Example: `nextflow run nf-core/airrflow -r 4.3.0 -profile test,singularity --outdir airrflow test
7. Prepare necessary inputs
   • samplesheets
   • path to input files (e.g. fastq.gz)
   • path to config file
8. Run according to recommended specs for project.