Snakefile

# ------------------------------------------------------------------------------
# Perform the TFBS enrichment for the EPIC replication
# ------------------------------------------------------------------------------
rule tfbs_enrichment_epic:
	input:
		cpg_annot = "cpg_annotation_both_arrays.tsv",
		meqtls = "sentinels_with_trans_epic.tsv",
		tfbs_granges = "tfbs_granges.RData",
	output:
		tfbs_annot = "epic_cpgs_with_chipseq_context_100_resample_{nresample}_{cpg_subset}.RData",
		result = "enrichment_chipseq_epic_context_100_resample_{nresample}_{cpg_subset}.txt"
	wildcard_constraints:
		nresample = "[0-9]+"
	threads:
		21
	resources:
		mem_mb = 1000
	params:
		time = "1-00:00:00"
	log:
		"logs/tfbs_enrichment_epic_resample_{nresample}_{cpg_subset}.log"
	benchmark:
		"benchmarks/tfbs_enrichment_epic_resample_{nresample}_{cpg_subset}.bmk"
	script:
		"R/tfbs-enrichment-epic.R"


rule tfbs_enrichment_epic_10000:
	input:
		"enrichment_chipseq_epic_context_100_resample_10000_450konly.txt",
		"enrichment_chipseq_epic_context_100_resample_10000_450kwith450kBG.txt",
		"enrichment_chipseq_epic_context_100_resample_10000_450kwithEPIC.txt",
		"enrichment_chipseq_epic_context_100_resample_10000_EPICFull.txt",
		"enrichment_chipseq_epic_context_100_resample_10000_EPICnoNovel.txt"