added VENN target

scripts/snakefiles/workflows/integration_ChIP_RNA.wf

@@ -23,10 +23,6 @@ subworkflow rna:
     configfile: config["RNA_seq"]["configfile"]
 
 
-## Test include
-#include: os.path.join(config["ChIP_seq"]["snakefile"])
-
-
 # from chip
 GENE_LIST = expand(expand(PEAKS_DIR + "/{treat}_vs_{control}/{{peakcaller}}/{treat}_vs_{control}_{{prefix}}_{{peakcaller}}_{{distance}}_annot_gene_list.tab", zip, treat=TREATMENT, control=CONTROL), peakcaller=PEAKCALLING_TOOLS, distance=DISTANCE,prefix=PREFIX)
 
@@ -36,6 +32,8 @@ GENE_LIST = expand(expand(DEG_DIR + "/{test}_vs_{ref}/{{deg}}/{test}_vs_{ref}_{{
 # Combined workflow
 VENN = "/data/analyses/Combined_ChIP-seq_RNA-seq/venn.png"
 
+VENN_DIAGS = "venn/{{prefix}}_{{peakcaller}}_{{distance}}_{{read_counts}}_{{deg}}
+
 rule all:
     input: VENN
 
@@ -45,7 +43,7 @@ rule venn:
     """This draft rule takes 3 inputs and creates a Venn Diagram:
         - a gene_list generated by the ChIP-seq workflow (genes intersecting with peaks associated with FNR binding, see dataset GSE41187)
         - a gene_list generated by the RNA-seq workflow (genes differentially expressed in FNR mutants, see dataset GSE41190)
-        - a gene_list manually generated from RegulonDB data (genes regulated by the FNR regulon, according to curated database RegulonDB)
+        - a gene_list manually generated from RegulonDB data (genes regulated by the FNR regulon, according to curated database RegulonDB) (optional)
     """
     input:
         chip_genes = chip("/data/analyses/ChIP-seq_SE_GSE41187/results/peaks/GSM1010219_vs_GSM1010224/homer-fdr0.001/GSM1010219_vs_GSM1010224_sickle_bowtie2_homer-fdr0.001_intersect_annot_gene_list.tab"),