BinAC/Software/Nextflow

Description

Nextflow is a scientific workflow system predominantly used for bioinformatic data analyses. This documentation also addresses nf-core, which is a community effort to collect a curated set of analysis pipelines built using Nextflow.

Installation

There is no environment module for Nextflow on the BinAC. We encourage users to install Nextflow via Miniconda. As Nextflow is often used with nf-core pipelines, we also recommend to install the nf-core tools.

The following commands will create a new Conda environment that provides Nextflow and nf-core tools. It also sets a Singularity cache directory where all Singularity containers are stored.

conda create --name nf-core python nf-core nextflow

echo "export NXF_SINGULARITY_CACHEDIR=/beegfs/work/container/apptainer_cache" >> ~/.bashrc
echo "export SINGULARITY_CACHEDIR=/beegfs/work/tu_iioba01/apptainer_cache " >> ~/.bashrc
source ~/.bashrc

conda activate nf-core

Usage

Install a nf-core pipeline

You could start and run pipelines now and the pipeline will pull all containers themselves. But we experienced problems when a pipeline started more than one job that pulls the same image. Thus we recommend to download the pipeline first using the nf-core tools. In this example we will use the rnaseq pipeline. If you need another pipeline,

nf-core download -x none -d -u amend --container-system singularity -r 3.14.0 rnaseq

nf-core tools can download pipelines and also download Singularity containers.

Run tests

The first thing you should do after downloading the pipeline is a test run. nf-core pipelines come with a test profile, which should just work out of the box. Also, there is a BinAC profile for nf-core. This profile contains settings for BinAC's job scheduler and queue settings.

nextflow run nf-core-rnaseq_3.14.0/3_14_0/ -profile binac,test --outdir /beegfs/work/tu_iioba01/nextflow_tests/results/