icbi-lab / nf-deseq2

A RNA-seq differential expression analysis pipeline downstream of nf-core/rnaseq.

nf-deseq2

A RNA-seq differential expression analysis pipeline downstream of nf-core/rnaseq.

Prerequisites

• Linux or MacOS, or Windows subsystem for Linux.
• Nextflow
• conda or mamba. If you don't have a conda installation, we recommend getting mambaforge.

Usage

TODO: Document how the pipeline can be ran and what input parameters it needs.

Output

TODO: Document the pipeline's output files and how to interpret them.

Developer docs

Setting up the editor

• If you are working with VSCode, we recommend installing the nf-core-extensionpack which makes it easier to work with nextflow files. See also the docs on nf-co.re

Running tests

• To run the pipeline on the testdata, run

  nextflow run main.nf -c tests/test.config

• To run the exact same tests as on the continuous integration, you need to install pytest-workflow

  pip install pytest-workflow

  Then, to run the tests and verify the outputs, run

  pytest --tag deseq2 --kwdof