Merge pull request #5 from aweich/cmod

Cmod

Author: aweich

workflow/Snakefile

@@ -31,8 +31,7 @@ if "functional_genomics" in config:
 	import VIS_functional_genomics_helper_functions as vhf_fg
 	include: config["functional_genomics"]
 	conditional_output.append(expand(f"{outdir}/final/functional_genomics/Functional_distances_to_Insertions_{{sample}}.bed", sample=SAMPLES))
-	conditional_output.append(expand(f"{outdir}/final/functional_genomics/Functional_distances_to_Insertions_{{sample}}.bed", sample=SAMPLES))
-	conditional_output.append(expand(f"{outdir}/intermediate/localization/annotation/Annotation_{{annotation}}_Insertions_{{sample}}.bed",
+	conditional_output.append(expand(f"{outdir}/intermediate/functional_genomics/Annotation_{{annotation}}_Insertions_{{sample}}.bed",
 									annotation=[k.replace("annotate_", "") for k in config if k.startswith("annotate_")],
 									sample=SAMPLES))
 

workflow/rules/functional_genomics.smk

@@ -46,7 +46,7 @@ rule annotation_overlap_insertion:
     log:
         log=f"{outdir}/intermediate/log/functional_genomics/annotation_overlap_insertion/{{sample}}.log"
     output:
-        **{k.replace("annotate_", ""): f"{outdir}/intermediate/localization/annotation/Annotation_{k.replace('annotate_', '')}_Insertions_{{sample}}.bed"
+        **{k.replace("annotate_", ""): f"{outdir}/intermediate/functional_genomics/Annotation_{k.replace('annotate_', '')}_Insertions_{{sample}}.bed"
            for k in config if k.startswith("annotate_")}
     run:
         vhf_fg.run_bedtools_intersect(input.insertions_bed, output, log.log, params.annotation_files)