Basic usage of PARANOiD

Description on how to the minimal set of PARANOiD. This means running it with only a FASTQ file containing reads, a reference genome and a barcode file. Generated outputs include alignments, cross-link sites in 3 different file types, an overview of the peak height distribution, :ref:` processing statistics <output-statistics>`, strand distributions and an IGV session which can be loaded directly into thr IGV to visualize first results. A directory with the name output (unless stated otherwise) containing all results will be generated. All parts marked with <> are files that need to be specified by the user

nextflow /path/to/directory/PARANOiD.nf --reads <read-file> --reference <reference-file> --barcodes <barcode-file> --omit_peak_calling --omit_peak_distance --omit_sequence_extraction