From 60c92b279e5b8b7cebd90c1f2c68c2619b7dcdf6 Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Mon, 18 Mar 2024 14:51:16 +0100
Subject: [PATCH] Add changelog description, add config keyword and reorder
 lines

---
 CHANGELOG.md                | 2 ++
 src/gffread/config.vsh.yaml | 2 +-
 src/gffread/test.sh         | 8 ++++----
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bd6a639a..e987a225 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,6 +29,8 @@
 
 * `star/star_align_reads`: Align reads to a reference genome (PR #22).
 
+* `gffread`: Validate, filter, convert and perform other operations on GFF files (PR #25). 
+
 ## MAJOR CHANGES
 
 ## MINOR CHANGES
diff --git a/src/gffread/config.vsh.yaml b/src/gffread/config.vsh.yaml
index 4ac2932d..705b8cb4 100644
--- a/src/gffread/config.vsh.yaml
+++ b/src/gffread/config.vsh.yaml
@@ -1,7 +1,7 @@
 name: gffread
 namespace: gffread
 description: Validate, filter, convert and perform various other operations on GFF files.
-keywords: [gff, conversion, validation]
+keywords: [gff, conversion, validation, filtering]
 links:
   homepage: https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
   documentation: https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
diff --git a/src/gffread/test.sh b/src/gffread/test.sh
index dcbad6bc..c7553839 100755
--- a/src/gffread/test.sh
+++ b/src/gffread/test.sh
@@ -92,6 +92,8 @@ diff "$expected_output_dir/transcripts.fa" "$test_output_dir/transcripts.fa" ||
 
 echo "> Test 4 - Generate table from GFF annotation file"
 
+# reference output annotation.tbl was created manually with gffread 0.12.7
+
 "$meta_executable" \
   --table @id,@chr,@start,@end,@strand,@exons,Name,gene,product \
   --outfile "$test_output_dir/annotation.tbl" \
@@ -109,12 +111,10 @@ echo ">> Compare output to expected output"
 diff "$expected_output_dir/annotation.tbl" "$test_output_dir/annotation.tbl" || \
     (echo "Output file annotation.tbl does not match expected output" && exit 1)
 
-# reference output annotation.tbl was created manually with gffread 0.12.7
-
 ################################################################################
 
-echo "> All tests successful"
-
 rm -r "$test_output_dir"
 
+echo "> All tests successful"
+
 exit 0
\ No newline at end of file