Fix file names and make output a required argument

emmarousseau · Mar 27, 2024 · aefe580 · aefe580
1 parent c26122e
commit aefe580
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/src/samtools/flagstat/config.vsh.yaml b/src/samtools/flagstat/config.vsh.yaml
@@ -28,6 +28,7 @@ argument_groups:
       description: |
         File containing samtools stats output.
       direction: output
+      required: true
       example: output.flagstat
 
 resources:

diff --git a/src/samtools/flagstat/test.sh b/src/samtools/flagstat/test.sh
@@ -15,7 +15,7 @@ echo ">>> Checking whether output is non-empty"
 
 echo ">>> Checking whether output is correct"
 diff "$meta_resources_dir/test_data/a.flagstat" "$meta_resources_dir/test_data/a_ref.flagstat" || \
-    (echo "Output file chr19.flagstat does not match expected output" && exit 1)
+    (echo "Output file ca.flagstat does not match expected output" && exit 1)
 
 rm "$meta_resources_dir/test_data/a.flagstat"
 
@@ -36,7 +36,7 @@ echo ">>> Checking whether output is non-empty"
 
 echo ">>> Checking whether output is correct"
 diff "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat" "$meta_resources_dir/test_data/test_ref.paired_end.sorted.flagstat" || \
-    (echo "Output file chr19.flagstat does not match expected output" && exit 1)
+    (echo "Output file test.pared_end.sorted.flagstat does not match expected output" && exit 1)
 
 rm "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat"