From 8b4d65bbd965ed3a39de81dcd0841699e41a5959 Mon Sep 17 00:00:00 2001
From: Anne Marie Noronha <anoronh4@users.noreply.github.com>
Date: Fri, 16 Jun 2023 12:35:50 -0400
Subject: [PATCH] Added patch to umitools/extract where output channel glob
 excludes input fastq

---
 modules.json                                       |  3 ++-
 modules/nf-core/umitools/extract/main.nf           |  2 +-
 .../nf-core/umitools/extract/umitools-extract.diff | 14 ++++++++++++++
 3 files changed, 17 insertions(+), 2 deletions(-)
 create mode 100644 modules/nf-core/umitools/extract/umitools-extract.diff

diff --git a/modules.json b/modules.json
index b0c405c..5d1c1d4 100644
--- a/modules.json
+++ b/modules.json
@@ -144,7 +144,8 @@
                     "umitools/extract": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/umitools/extract/umitools-extract.diff"
                     }
                 }
             },
diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf
index 2f94fa9..77d7435 100644
--- a/modules/nf-core/umitools/extract/main.nf
+++ b/modules/nf-core/umitools/extract/main.nf
@@ -12,7 +12,7 @@ process UMITOOLS_EXTRACT {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.fastq.gz"), emit: reads
+    tuple val(meta), path("*.umi_extract*.fastq.gz"), emit: reads
     tuple val(meta), path("*.log")     , emit: log
     path  "versions.yml"               , emit: versions
 
diff --git a/modules/nf-core/umitools/extract/umitools-extract.diff b/modules/nf-core/umitools/extract/umitools-extract.diff
new file mode 100644
index 0000000..317dabb
--- /dev/null
+++ b/modules/nf-core/umitools/extract/umitools-extract.diff
@@ -0,0 +1,14 @@
+Changes in module 'nf-core/umitools/extract'
+--- modules/nf-core/umitools/extract/main.nf
++++ modules/nf-core/umitools/extract/main.nf
+@@ -12,7 +12,7 @@
+     tuple val(meta), path(reads)
+ 
+     output:
+-    tuple val(meta), path("*.fastq.gz"), emit: reads
++    tuple val(meta), path("*.umi_extract*.fastq.gz"), emit: reads
+     tuple val(meta), path("*.log")     , emit: log
+     path  "versions.yml"               , emit: versions
+ 
+
+************************************************************