Snakefile1

path="/data/compbio/inathoo/snakemake_test/test4/"

rule get_ids:
	input:
		expand(path+"data")
	output:
		directory(expand(path+"deg_sets/gene_ids"))
	shell:
		"./scripts/all_csv_to_id.sh {input}"

rule find_intersections:
	input:
		expand(path+"deg_sets/gene_ids")
	output:
		directory(expand(path+"deg_sets/barPlot"))
	shell:
		"intervene upset -i {input}/*.txt --type list --save-overlaps --figtype png -o '{input}/../barPlot'"

rule get_gene:
	input:
		expand(path+"deg_sets/gene_ids")
	output:
		directory(expand(path+"deg_sets/gene_beds"))
	shell:
		"./scripts/all_id_to_gene.sh {input}"

rule make_boxplots:
	input:
		expand(path+"deg_sets/gene_beds")
	output:
		directory(expand(path+"comparisons/overall_boxplots"))
	shell:
		"python /scripts/allBoxPlots.py -f {input}"	

rule make_XAboxplots:
	input:
		expand(path+"deg_sets/gene_beds")
	output:
		directory(expand(path+"comparisons/xa_boxplots"))
	shell:
		"python /scripts/xaBoxPlotsfinal.py -f {input} -s {output}"	

rule global_boxplots:
	input:
		expand(path+"data")
	output:
		directory(expand(path+"comparisons/global_boxplots"))
	shell:
		"python /scripts/global_XAv5.py -f {input} -m []"