Also generate bedgraph.

bigwig_average_over_bed/wrapper.py

@@ -3,7 +3,7 @@ from libworkflows import run_with_modules
 
 load_modules = snakemake.config.get("load_modules", False)
 if load_modules:
-    modules = ["UCSC-tools/v373"]
+    modules = ["bioawk", "UCSC-tools/v373"]
 else:
     modules = []
 
@@ -14,7 +14,9 @@ bigWigAverageOverBed \\
     {snakemake.params.genome_binned} \\
     /dev/null \\
     2> {snakemake.log.err}
+    bioawk -t '{{print $1,$2,$3,$5}}' {snakemake.output.bed} \\
+        2>> {snakemake.log.err} \\
+        > {snakemake.output.bedgraph}
 """
 
-#run_with_modules(shell_commands, modules)
 shell(run_with_modules(shell_commands, modules))