nf-template

Nextflow template for fast pipeline generation

Installation

Dependencies

Look at environment.yml for the individual dependencies for running nextflow. The pipeline also supports Slurm (>= 20.11.4) if you want to process larger cohorts.

Download

git clone [email protected]:TRON-Bioinformatics/nf-template.git

Configure Environment

cd nf-template
conda env create -f environment.yml --prefix conda_env/

References

Specify pathes to your references in your nextflow.config.

Usage

Prepare your input table

The pipeline requires comma-separated, headerless input table of the following format:

Sample_01	fastq1	fastq2
Sample_02	fastq1	fastq2

Start pipeline

source /path/to/your/miniconda3/bin/activate /path/to/conda_env
nextflow run main.nf -profile [standard|cluster] --input_table <path_to_input_table> --output <path_to_output>