From f4a05b135be7013512b0b139593549aef58f5b75 Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Thu, 21 Mar 2024 10:57:38 +0100
Subject: [PATCH] Make output file argument required

---
 src/gffread/config.vsh.yaml | 1 +
 src/gffread/script.sh       | 2 +-
 src/gffread/test.sh         | 1 +
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/gffread/config.vsh.yaml b/src/gffread/config.vsh.yaml
index 009b852a..e4ee2fd3 100644
--- a/src/gffread/config.vsh.yaml
+++ b/src/gffread/config.vsh.yaml
@@ -51,6 +51,7 @@ argument_groups:
         type: file
         direction: output
         must_exist: false
+        required: true
         description: |
           Write the output records into <outfile>.
         default: output.gff
diff --git a/src/gffread/script.sh b/src/gffread/script.sh
index 47a45267..26986fd1 100644
--- a/src/gffread/script.sh
+++ b/src/gffread/script.sh
@@ -55,7 +55,7 @@ gffread \
     "$par_input" \
     ${par_chr_mapping:+-m "$par_chr_mapping"} \
     ${par_seq_info:+-s "$par_seq_info"} \
-    ${par_outfile:+-o "$par_outfile"} \
+    -o "$par_outfile" \
     ${par_force_exons:+--force-exons} \
     ${par_gene2exon:+--gene2exon} \
     ${par_t_adopt:+--t-adopt} \
diff --git a/src/gffread/test.sh b/src/gffread/test.sh
index 5eebe9a6..6d38012b 100755
--- a/src/gffread/test.sh
+++ b/src/gffread/test.sh
@@ -66,6 +66,7 @@ echo "> Test 3 - Generate fasta file from annotation file"
 "$meta_executable" \
   --genome "$test_dir/sequence.fasta" \
   --spliced_exons "$test_output_dir/transcripts.fa" \
+  --outfile "$test_output_dir/output.gff" \
   --input "$test_dir/sequence.gff3"
 
 echo ">> Check if output exists"