From 1fb1801dcbbc556d04985bda5ba4329a4f50543f Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Fri, 25 Mar 2022 08:54:09 -0500
Subject: [PATCH] refactor(homer): Update output path for bedGraph (#1438)

This allow for caching because otherwise it modifies the tag directory input
---
 modules/homer/makeucscfile/main.nf        | 6 +++---
 modules/homer/makeucscfile/meta.yml       | 2 +-
 tests/modules/homer/makeucscfile/test.yml | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/homer/makeucscfile/main.nf b/modules/homer/makeucscfile/main.nf
index c82435ea..379fad3d 100644
--- a/modules/homer/makeucscfile/main.nf
+++ b/modules/homer/makeucscfile/main.nf
@@ -13,8 +13,8 @@ process HOMER_MAKEUCSCFILE {
     tuple val(meta), path(tagDir)
 
     output:
-    tuple val(meta), path("tag_dir/*ucsc.bedGraph.gz"), emit: bedGraph
-    path  "versions.yml"                              , emit: versions
+    tuple val(meta), path("*.bedGraph.gz"), emit: bedGraph
+    path  "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,7 +25,7 @@ process HOMER_MAKEUCSCFILE {
     """
     makeUCSCfile \\
         $tagDir \\
-        -o auto \\
+        -o ${prefix}.bedGraph \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/homer/makeucscfile/meta.yml b/modules/homer/makeucscfile/meta.yml
index 273f456e..039fd37f 100644
--- a/modules/homer/makeucscfile/meta.yml
+++ b/modules/homer/makeucscfile/meta.yml
@@ -30,7 +30,7 @@ output:
   - bedGraph:
       type: file
       description: The UCSC bed graph
-      pattern: "tag_dir/*ucsc.bedGraph.gz"
+      pattern: "*.bedGraph.gz"
   - versions:
       type: file
       description: File containing software versions
diff --git a/tests/modules/homer/makeucscfile/test.yml b/tests/modules/homer/makeucscfile/test.yml
index cf3d1b4d..e6ccb9fa 100644
--- a/tests/modules/homer/makeucscfile/test.yml
+++ b/tests/modules/homer/makeucscfile/test.yml
@@ -4,4 +4,4 @@
     - homer
     - homer/makeucscfile
   files:
-    - path: output/homer/tag_dir/tag_dir.ucsc.bedGraph.gz
+    - path: output/homer/test.bedGraph.gz