From f3d8cd7d54c0db3e644f7c3efbcea4fa962d05c3 Mon Sep 17 00:00:00 2001
From: Nathan Spix <56930974+njspix@users.noreply.github.com>
Date: Tue, 14 Feb 2023 14:16:33 -0500
Subject: [PATCH 1/2] remove unused output folder

---
 conf/modules.config | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index f9c155ae..1827da52 100755
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -229,11 +229,6 @@ process {
                 mode: params.publish_dir_mode,
                 pattern: "*bedGraph.gz"
             ],
-            [
-                path: { "${params.outdir}/${params.aligner}/methylation_calls/stranded_CpG_report" },
-                mode: params.publish_dir_mode,
-                pattern: "*CpG_report.txt.gz"
-            ],
             [
                 path: { "${params.outdir}/${params.aligner}/methylation_calls/splitting_report" },
                 mode: params.publish_dir_mode,

From 375ae9625546b44582fabd76f20c149ef244c261 Mon Sep 17 00:00:00 2001
From: Nathan Spix <56930974+njspix@users.noreply.github.com>
Date: Tue, 14 Feb 2023 14:27:07 -0500
Subject: [PATCH 2/2] remove additional unused directory

---
 conf/modules.config | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 1827da52..db8ae124 100755
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -245,11 +245,6 @@ process {
     withName: BISMARK_COVERAGE2CYTOSINE {
         ext.args = params.nomeseq ? '--nome-seq' : ''
         publishDir = [
-            [
-                path: { "${params.outdir}/bismark/coverage2cytosine/coverage" },
-                mode: params.publish_dir_mode,
-                pattern: "*.cov.gz"
-            ],
             publishDir = [
                 path: { "${params.outdir}/bismark/coverage2cytosine/summaries" },
                 mode: params.publish_dir_mode,