From e6d9190fbba355ffa8d47ee0e67c9b98bbb8418e Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lorena.pantano@gmail.com>
Date: Mon, 15 Jul 2024 14:52:49 -0400
Subject: [PATCH] remove bam to bed

---
 .../bam_peaks_call_qc_annotate_macs2_homer.nf | 21 +------------------
 1 file changed, 1 insertion(+), 20 deletions(-)

diff --git a/subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer.nf b/subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer.nf
index 633bb3cc..5b7b9b85 100644
--- a/subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer.nf
+++ b/subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer.nf
@@ -2,7 +2,6 @@
 // Call peaks with MACS2, annotate with HOMER and perform downstream QC
 //
 
-include { BEDTOOLS_BAMTOBED        } from '../../modules/nf-core/bedtools/bamtobed/main'
 include { MACS2_CALLPEAK           } from '../../modules/nf-core/macs2/callpeak/main'
 include { HOMER_ANNOTATEPEAKS      } from '../../modules/nf-core/homer/annotatepeaks/main'
 
@@ -29,29 +28,11 @@ workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS2_HOMER {
 
     ch_versions = Channel.empty()
 
-    //
-    // Convert bam to bed
-    //
-    BEDTOOLS_BAMTOBED (
-      ch_bam.map { meta, ip_bam, control_bam -> [ meta, ip_bam ] }
-    )
-    ch_versions = ch_versions.mix(BEDTOOLS_BAMTOBED.out.versions.first())
-
-    // Create channels: [meta, ip_bed, []]
-    BEDTOOLS_BAMTOBED
-        .out
-        .bed
-        .map {
-            meta, ip_bed -> 
-                [ meta, ip_bed, [] ] 
-        }
-        .set { ch_bed }
-    
     //
     // Call peaks with MACS2
     //
     MACS2_CALLPEAK (
-        ch_bed,
+        ch_bam,
         macs_gsize
     )
     ch_versions = ch_versions.mix(MACS2_CALLPEAK.out.versions.first())