Installation

To run PARANOiD users need to have Nextflow installed along with one of the supported container runtimes mentioned in the container section. PARANOiD can be downloaded manually from the GitHub repository PARANOID or via the command line:

git clone https://github.com/patrick-barth/PARANOID

Alternatively PARANOiD can be launched directly via the following command, which automatically downloads the workflow to <HOME>/.nextflow/assets/patrick-barth/PARANOiD:

nextflow run patrick-barth/PARANOiD -r main --reads reads.fastq --reference reference.fasta --barcodes barcodes.tsv --output output --omit_peak_calling --omit_peak_distance --omit_sequence_extraction  -profile apptainer