From 8eb8271d495815b0131b4009665804f7975a5009 Mon Sep 17 00:00:00 2001
From: samuelruizperez <samuel.ruiz.perez@outlook.com>
Date: Fri, 1 Sep 2023 10:45:56 +0200
Subject: [PATCH] fixing peak annotation dirs

---
 conf/modules.config | 53 ++++++++++++++++++++++-----------------------
 1 file changed, 26 insertions(+), 27 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index f737435e..b38e0535 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -1134,46 +1134,45 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+}
 
-    if (!params.skip_peak_annotation) {
+if (!params.skip_peak_annotation) {
+    process {
+        withName: '.*:MERGED_LIBRARY_JOINT_CALL_ANNOTATE_PEAKS_GENRICH:HOMER_ANNOTATEPEAKS' {
+            ext.args   = '-gid'
+            ext.prefix = { "${meta.id}.mLb.genrich.jpeaks" }
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}/merged_library/genrich/joint/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+    }
+
+    if (!params.skip_peak_qc) {
         process {
-            withName: '.*:MERGED_LIBRARY_JOINT_CALL_ANNOTATE_PEAKS_GENRICH:HOMER_ANNOTATEPEAKS' {
-                ext.args   = '-gid'
-                ext.prefix = { "${meta.id}.mLb.genrich.jpeaks" }
+            withName: '.*:MERGED_LIBRARY_JOINT_CALL_ANNOTATE_PEAKS_GENRICH:PLOT_GENRICH_QC' {
+                ext.args   = '-o ./ -p genrich_jpeak.mLb'
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/merged_library/genrich/joint/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/genrich/joint/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
             }
-        }
 
-        if (!params.skip_peak_qc) {
-            process {
-                withName: '.*:MERGED_LIBRARY_JOINT_CALL_ANNOTATE_PEAKS_GENRICH:PLOT_GENRICH_QC' {
-                    ext.args   = '-o ./ -p genrich_jpeak.mLb'
-                    publishDir = [
-                        path: { "${params.outdir}/${params.aligner}/merged_library/genrich/joint/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
-                        mode: params.publish_dir_mode,
-                        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                    ]
-                }
-
-                withName: '.*:MERGED_LIBRARY_JOINT_CALL_ANNOTATE_PEAKS_GENRICH:PLOT_HOMER_ANNOTATEPEAKS' {
-                    ext.args   = '-o ./'
-                    ext.prefix = 'genrich_annotate_jPeaks.mLb'
-                    publishDir = [
-                        path: { "${params.outdir}/${params.aligner}/merged_library/genrich/joint/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
-                        mode: params.publish_dir_mode,
-                        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                    ]
-                }
+            withName: '.*:MERGED_LIBRARY_JOINT_CALL_ANNOTATE_PEAKS_GENRICH:PLOT_HOMER_ANNOTATEPEAKS' {
+                ext.args   = '-o ./'
+                ext.prefix = 'genrich_annotate_jPeaks.mLb'
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/merged_library/genrich/joint/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
             }
         }
     }
 }
 
-
 if (!params.skip_igv) {
     process {
         withName: 'IGV' {