Test Script

src/bedtools/bedtools_bamtofastq/config.vsh.yaml

@@ -31,16 +31,16 @@ argument_groups:
         type: file
         description: Output FASTQ file.
         required: true
-
-  - name: Options
-    arguments:
+
       - name: --output_fq2
         alternatives: -fq2
         type: file
         description: |
           FASTQ for second end.  Used if BAM contains paired-end data.
           BAM should be sorted by query name is creating paired FASTQ.
-
+         
+  - name: Options
+    arguments:
       - name: --tags
         type: boolean_true
         description: |

src/bedtools/bedtools_bamtofastq/test.sh

@@ -1,5 +1,56 @@
 #!/bin/bash
 
-#viash ns build -q bedtools_bamtofastq --setup cb
+# viash ns build -q bedtools_bamtofastq --setup cb
 
+# exit on error
+set -e
 
+## VIASH START
+meta_executable="target/executable/bedtools/bedtools_sort/bedtools_bamtofastq"
+meta_resources_dir="src/bedtools/bedtools_bamtofastq"
+## VIASH END
+
+#############################################
+# helper functions
+assert_file_exists() {
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
+}
+assert_file_not_empty() {
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
+}
+assert_file_contains() {
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
+}
+assert_identical_content() {
+  diff -a "$2" "$1" \
+    || (echo "Files are not identical!" && exit 1)
+}
+#############################################
+
+# Create directories for tests
+echo "Creating Test Data..."
+mkdir -p test_data
+
+# Create and populate example files
+
+# Create expected output files
+
+
+# Test 1: 
+mkdir test1
+cd test1
+
+echo "> Run bedtools bamtofastq on BAM file"
+"$meta_executable" \
+  --input "example.bam" \
+  --output_fq "output.fastq"
+
+# checks
+assert_file_exists "output.fastq"
+assert_file_not_empty "output.fastq"
+assert_identical_content "output.fastq" "../test_data/expected.fastq"
+echo "- test1 succeeded -"
+
+cd ..
+
+# Test 2: