VizFaDa ChIP-seq pipeline

A Nextflow pipeline to download FAANG ChIP-seq data, launch the nf-co.re/chipseq in batch, and clean behind it by removing heavy fastq & bam files, and the Nextflow work directory.

Used to process all FAANG ChIP-seq files for the VizFaDa project.

Usage

At the moment, the pipeline only runs on the Genotoul compute server due to the hard-coded launch of the nfcore/chipseq command here.

Example usage:

nextflow run lauramble/chipseq_vizfada --species 'Sus scrofa' -profile genotoul -with-report -with-trace -with-timeline -resume

This command will download metadata for all FAANG pig ChIP-seq, then for each distinct ChIP-seq input file, will:

• dowload .fastq files from ENA for the Input and each associated Bound samples.
• run nf-core/chipseq on these files
• remove the dowloaded fastq and bam files, as well as the temporary nextflow /work folder, to prevent disk saturation
• move on to the next Input sample

Pipeline tuning

Reference genomes

Reads will be align to Ensembl reference genomes (automatically retrieved at the begining of the pipeline) as specified by this configuration file.