refactor: Replace local bedtools genomecov module with nf-core version

- Replace local bedtools_genomecov module with nf-core bedtools/genomecov
- Add inline scale factor calculation from flagstat in subworkflow
- Configure nf-core module with -bga and -pc flags for proper output
- Remove scale_factor output emit as it's no longer needed
- Maintain same functionality while using official nf-core modules

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: edmundmiller

conf/modules.config

@@ -459,6 +459,10 @@ process {
             if (meta.single_end && params.fragment_size > 0) {
                 args << "-fs ${params.fragment_size}"
             }
+            // Add paired-end correction for paired-end data
+            if (!meta.single_end) {
+                args << "-pc"
+            }
             // Use -bga instead of -bg to include zero-coverage bins
             // This results in lower background levels and better IGV visualization
             args << "-bga"

modules/local/bedtools_genomecov.nf

@@ -2,7 +2,7 @@
 // Convert BAM to normalised bigWig via bedGraph using BEDTools and UCSC
 //
 
-include { BEDTOOLS_GENOMECOV    } from '../../modules/local/bedtools_genomecov'
+include { BEDTOOLS_GENOMECOV    } from '../../modules/nf-core/bedtools/genomecov/main'
 include { UCSC_BEDGRAPHTOBIGWIG } from '../../modules/nf-core/ucsc/bedgraphtobigwig/main'
 
 workflow BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC {
@@ -14,11 +14,26 @@ workflow BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC {
 
     ch_versions = Channel.empty()
 
+    //
+    // Extract scale factor from flagstat and prepare input for bedtools genomecov
+    //
+    ch_bam_scale = ch_bam_flagstat
+        .map { meta, bam, flagstat -> 
+            // Parse flagstat to get mapped reads count
+            def flagstat_content = flagstat.text
+            def mapped_reads = (flagstat_content =~ /(\d+) \+ \d+ mapped/)[0][1] as Integer
+            def scale_factor = 1000000 / mapped_reads
+            [meta, bam, scale_factor]
+        }
+
     //
     // Create bedGraph coverage track
     //
     BEDTOOLS_GENOMECOV (
-        ch_bam_flagstat
+        ch_bam_scale,
+        [],
+        'bedGraph',
+        true
     )
     ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions.first())
 
@@ -32,9 +47,7 @@ workflow BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC {
     ch_versions = ch_versions.mix(UCSC_BEDGRAPHTOBIGWIG.out.versions.first())
 
     emit:
-    bedgraph     = BEDTOOLS_GENOMECOV.out.bedgraph      // channel: [ val(meta), [ bedgraph ] ]
-    scale_factor = BEDTOOLS_GENOMECOV.out.scale_factor  // channel: [ val(meta), [ txt ] ]
-
+    bedgraph     = BEDTOOLS_GENOMECOV.out.genomecov     // channel: [ val(meta), [ bedgraph ] ]
     bigwig       = UCSC_BEDGRAPHTOBIGWIG.out.bigwig     // channel: [ val(meta), [ bigwig ] ]
 
     versions     = ch_versions                          // channel: [ versions.yml ]