Make output file argument required

emmarousseau · Mar 21, 2024 · f4a05b1 · f4a05b1
1 parent f522635
commit f4a05b1
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Showing 3 changed files with 3 additions and 1 deletion.
diff --git 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
@@ -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
@@ -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"