From d6d1d2cff87db3cc48c278ad3ffc70b12f499f8a Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Wed, 27 Sep 2023 10:46:34 +0100
Subject: [PATCH 1/3] Deal with factor names on unified factor file

---
 tools/edger/edger.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/edger/edger.R b/tools/edger/edger.R
index 0d8be1d901b..4517ad34542 100644
--- a/tools/edger/edger.R
+++ b/tools/edger/edger.R
@@ -283,7 +283,7 @@ if (!is.null(opt$filesPath)) {
     }
     # order samples as in counts matrix
     factordata <- factordata[match(colnames(counts), factordata[, 1]), ]
-    factors <- factordata[, -1, drop = FALSE]
+    factors <- sapply(factordata[, -1, drop = FALSE], make.names)
   } else {
     factors <- unlist(strsplit(opt$factInput, "|", fixed = TRUE))
     factordata <- list()

From c310dae6d2cf00451f5cd2cfccb550c8fe8819d8 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Wed, 27 Sep 2023 10:49:58 +0100
Subject: [PATCH 2/3] Bumps galaxy build number

---
 tools/edger/edger.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/edger/edger.xml b/tools/edger/edger.xml
index 137a599d688..ee7cad7e6b3 100644
--- a/tools/edger/edger.xml
+++ b/tools/edger/edger.xml
@@ -4,7 +4,7 @@
     </description>
     <macros>
         <token name="@TOOL_VERSION@">3.36.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <edam_topics>
         <edam_topic>topic_3308</edam_topic>

From 4b3d76504db1c2044e3dafcb4de1a1a23f008ec5 Mon Sep 17 00:00:00 2001
From: Pablo Moreno <pcm32@users.noreply.github.com>
Date: Wed, 27 Sep 2023 10:28:36 +0000
Subject: [PATCH 3/3] Make factors a data.frame

---
 tools/edger/edger.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/edger/edger.R b/tools/edger/edger.R
index 4517ad34542..1b0fdc96db9 100644
--- a/tools/edger/edger.R
+++ b/tools/edger/edger.R
@@ -283,7 +283,7 @@ if (!is.null(opt$filesPath)) {
     }
     # order samples as in counts matrix
     factordata <- factordata[match(colnames(counts), factordata[, 1]), ]
-    factors <- sapply(factordata[, -1, drop = FALSE], make.names)
+    factors <- data.frame(sapply(factordata[, -1, drop = FALSE], make.names))
   } else {
     factors <- unlist(strsplit(opt$factInput, "|", fixed = TRUE))
     factordata <- list()