This folder, resources/, is meant to contain all resources (except larger genome indexes) necessary for running the workflow. The subfolders are:
- blacklistFa: Blacklist BED files are downloaded for human (v3) and mouse (v1). Using the coordinates from these BED files, fasta sequences are extracted for hg19/39 and mm10.
- frip: BED files for DHS/enhancer/promoter locations for hg19/39 and mm10 genomes.
- motif: HOCOMOCO v11 motifs in HOMER and MEME formats for human and mouse.
- tssBed: BED files pin-pointing the transcription start sites of annotated genes for hg19/38 and mm10.
cluster.json file can make specific resource requests to biowulf via slurm. Each Snakemake rule can make a unique hardware request for slurm execution.
tools.yaml file would typically contain the modules required to be loaded for rule execution on the Biowulf cluster. Since we are using dockers for all rules in this pipeline, tools.yaml will be empty.