fix: Move bg to args

#470 (comment)

Co-authored-by: pinin4fjords <[email protected]>

Author: edmundmiller

conf/modules.config

@@ -453,7 +453,17 @@ process {
     }
 
     withName: '.*:BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC:BEDTOOLS_GENOMECOV' {
-        ext.args   = { (meta.single_end && params.fragment_size > 0) ? "-fs ${params.fragment_size}" : '' }
+        ext.args   = {
+            def args = []
+            // Include fragment size only for single-end data
+            if (meta.single_end && params.fragment_size > 0) {
+                args << "-fs ${params.fragment_size}"
+            }
+            // Use -bga instead of -bg to include zero-coverage bins
+            // This results in lower background levels and better IGV visualization
+            args << "-bga"
+            return args.join(' ')
+        }
         ext.prefix = { "${meta.id}.mLB.clN" }
         publishDir = [
             [

modules/local/bedtools_genomecov.nf

@@ -26,13 +26,9 @@ process BEDTOOLS_GENOMECOV {
     SCALE_FACTOR=\$(grep '[0-9] mapped (' $flagstat | awk '{print 1000000/\$1}')
     echo \$SCALE_FACTOR > ${prefix}.scale_factor.txt
 
-    # Use --bga instead of -bg to include zero-coverage bins in output
-    # This results in lower background levels and better visualization in IGV
-    # Users can override this by specifying -bg in ext.args if needed
     bedtools \\
         genomecov \\
         -ibam $bam \\
-        --bga \\
         -scale \$SCALE_FACTOR \\
         $pe \\
         $args \\