This repository contains a Nextflow pipeline for performing motif analysis in specific regions of the genome using Homer while subtracting a background.

The provided Nextflow pipeline automates the following steps:

1. runInitialHomer with an input background BED file.
2. cat_homer_results with the HOMER results files produced by the previous step.
3. runHomerInPeaks running Homer on the subject bed file, while subtracting the motifs found in the background BED file.
4. find_relevant_motifs.py find relevant motifs of TF, provided in keyTF.csv, in the result motifs.
5. convert_output_to_final_format.R to fit into same format as all TFBS tools.

params.backgroundBed

params.subjectBed

params.homerResults - results directory

params.bin - path to a directory containing scripts and additional files

params.tfListFile - a list of TF of interest

Run the pipeline using Nextflow:

nextflow WGS_DSD-HOMER/HOMER_peaks_analysis.nf --backgroundBed 'path/to/file.bed' --subjectBed 'path/to/file.bed' --homerResults 'results/path' --bin /path/to/WGS_DSD-HOMER/bin/