Adds help message for --mask_dir_{artifacts,cohort}

Author: viklund

README.md

@@ -71,6 +71,10 @@ Options:
     --no_sg_reciprocal  Don't use a reciprocal overlap for the filter option
     --outdir        Directory where resultfiles are stored (default: results)
     --prefix        Prefix for result filenames (default: no prefix)
+    --mask_dir_artifacts
+                    Directory with bed files for artifact filtering (default: mask_artifacts)
+    --mask_dir_cohort
+                    Directory with bed files for cohort filtering (default: mask_cohort)
 ```
 
 The log file `.nextflow.log` will be produced when running and can be monitored

main.nf

@@ -444,6 +444,10 @@ def usage_message() {
     log.info '    --no_sg_reciprocal  Don\'t use a reciprocal overlap for the filter option'
     log.info '    --outdir        Directory where resultfiles are stored (default: results)'
     log.info '    --prefix        Prefix for result filenames (default: no prefix)'
+    log.info '    --mask_dir_artifacts'
+    log.info '                    Directory with bed files for artifact filtering (default: mask_artifacts)'
+    log.info '    --mask_dir_cohort'
+    log.info '                    Directory with bed files for cohort filtering (default: mask_cohort)'
     log.info ''
 }