Day 4

Setting up a Nextflow rna-seq pipeline from nf-core
diary
Author

Joel Tekoniemi

Published

October 9, 2025

Nextflow

Pipeline setup

It is pretty easy to setup nextflow pipelines with the help of nf-core, but there is nonetheless some configuration that is needed: - Create Pixi environment - add channels conda-forge and bioconda -c conda-forge -c bioconda - add packages nextflow and nf-core - Create data folder and other necessary folder for pipeline E.g. genome, results, Symbolic link nl for data to avoid copying - Navigate to the nf-core pipeline and use the installer

Example using the rna-seq pipeline

pixi run nextflow run nf-core/rnaseq -r 3.19.0 -resume -params-file nf-params.json -c hpc2n.config

Image: rna-seq-pipeline

Image: rna-seq-pipeline

Fancy stuff

  • tags: tags are shown next to processes when running pipeline
  • workflow.onComplete: more info and user-friendly messages upon completed workflow