Nextflow template for fast pipeline generation
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.
git clone [email protected]:TRON-Bioinformatics/nf-template.git
cd nf-template
conda env create -f environment.yml --prefix conda_env/
Specify pathes to your references in your nextflow.config.
The pipeline requires comma-separated, headerless input table of the following format:
| Sample_01 | fastq1 | fastq2 |
| Sample_02 | fastq1 | fastq2 |
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>