first basic test working & changed source container for a more recent…

… version
emmarousseau · Mar 22, 2024 · 7846fe6 · 7846fe6
1 parent 8e3d5c5
commit 7846fe6
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/src/samtools/flagstat/config.vsh.yaml b/src/samtools/flagstat/config.vsh.yaml
@@ -40,7 +40,7 @@ test_resources:
     path: test_data
 engines:
   - type: docker
-    image: quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1
+    image: quay.io/biocontainers/samtools:1.3.1--h9071d68_10
     setup:
       - type: docker
         run: |

diff --git a/src/samtools/flagstat/script.sh b/src/samtools/flagstat/script.sh
@@ -5,7 +5,9 @@
 
 set -e
 
+output_file="$par_output"
+
 samtools flagstat \
-    "$par_input_bam" \
-    > "$par_output_stats"
+    "$par_bam" \
+    > "$output_file"
 
diff --git a/src/samtools/flagstat/test.sh b/src/samtools/flagstat/test.sh
@@ -8,14 +8,14 @@ echo ">>> Testing $meta_functionality_name"
   --output "$meta_resources_dir/test_data/chr19.flagstat"
 
 echo ">>> Checking whether output exists"
-[ ! -f "test_data/chr19.flagstat" ] && echo "File 'chr19.flagstat' does not exist!" && exit 1
+[ ! -f "$meta_resources_dir/test_data/chr19.flagstat" ] && echo "File 'chr19.flagstat' does not exist!" && exit 1
 
 echo ">>> Checking whether output is non-empty"
-[ ! -s "test_data/chr19.flagstat" ] && echo "File 'chr19.flagstat' is empty!" && exit 1
+[ ! -s "$meta_resources_dir/test_data/chr19.flagstat" ] && echo "File 'chr19.flagstat' is empty!" && exit 1
 
 echo ">>> Checking whether output is correct"
 diff "$meta_resources_dir/test_data/chr19.flagstat" "$meta_resources_dir/test_data/chr19_ref.flagstat" || \
-    (echo "Output does not match expected output." && exit 1)
+    (echo "Output file chr19.flagstat does not match expected output" && exit 1)
 
 rm "$meta_resources_dir/test_data/chr19.flagstat"