From 6aa60a6a898175fa1cd6d37b68259156c868c297 Mon Sep 17 00:00:00 2001
From: Leon Hafner <leon.hafner@tum.de>
Date: Tue, 9 Jan 2024 15:20:32 +0100
Subject: [PATCH] Integrate output of Rose into workflow and disable eHMM

---
 subworkflows/local/peaks.nf | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf
index 2c6d9241..8de6618a 100644
--- a/subworkflows/local/peaks.nf
+++ b/subworkflows/local/peaks.nf
@@ -71,6 +71,7 @@ workflow PEAKS {
         REMOVE_CHR(ch_footprints, [])
         ch_footprints_nochr = REMOVE_CHR.out.output
 
+        /*
         if (params.bam_design) {
             ch_bams = Channel.value(file(params.bam_design))
                                 .splitCsv(header: true)
@@ -101,7 +102,8 @@ workflow PEAKS {
 
             ch_footprints = EHMM.out.all
         }
-        
+        */
+
         if (params.bam_design2) {
             // Parse design file
             ch_bams = Channel.value(file(params.bam_design2))
@@ -139,6 +141,13 @@ workflow PEAKS {
             params.ucsc_file
         )
 
+        // Adapt process output to previous design of ch_footprints
+        ch_footprints = ROSE.out
+            .map{meta, bed -> 
+                meta = meta + [id: meta.state + "_enhancers", antibody: "enhancers"]
+                [meta, bed]
+            }
+
         }
         
         if (params.blacklist) {