Clean up test script, update changelog

CHANGELOG.md

@@ -36,8 +36,8 @@
     - `salmon/salmon_quant`: Transcript quantification from RNA-seq data (PR #24).
 
 * `samtools`:
-    - `samtools/flagstat`: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
-    - `samtools/idxstats`: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).    
+    - `samtools/samtools_flagstat`: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
+    - `samtools/samtools_idxstats`: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).    
     - `samtools/samtools_sort`: Sort SAM/BAM/CRAM files (PR #36).
 
 ## MAJOR CHANGES

src/samtools/samtools_sort/config.vsh.yaml

@@ -25,6 +25,7 @@ argument_groups:
         description: |
           Write final output to file.
         required: true
+        must_exist: false
         example: out.bam
       - name: --output_fmt
         alternatives: -O

src/samtools/samtools_sort/test.sh

@@ -14,15 +14,15 @@ echo ">>> Test 1: Sorting a BAM file"
 
 echo ">>> Check if output file exists"
 [ ! -f "$test_dir/a.sorted.bam" ] \
-    && echo "Output file test_data/a.sorted.bam does not exist" && exit 1
+    && echo "Output file a.sorted.bam does not exist" && exit 1
 
 echo ">>> Check if output is empty"
 [ ! -s "$test_dir/a.sorted.bam" ] \
-    && echo "Output file test_data/a.sorted.bam is empty" && exit 1
+    && echo "Output file a.sorted.bam is empty" && exit 1
 
 echo ">>> Check if output matches expected output"
 diff -a "$test_dir/a.sorted.bam.txt" "$out_dir/a_ref.sorted.txt" \
-    || (echo "Output file test_data/a.sorted.bam does not match expected output" && exit 1)
+    || (echo "Output file a.sorted.bam does not match expected output" && exit 1)
 
 rm "$test_dir/a.sorted.bam" "$test_dir/a.sorted.bam.txt"
 
@@ -37,15 +37,15 @@ echo ">>> Test 2: Sorting a BAM file according to ascii order"
 
 echo ">>> Check if output file exists"
 [ ! -f "$test_dir/ascii.sorted.bam" ] \
-    && echo "Output file test_data/ascii.sorted.bam does not exist" && exit 1
+    && echo "Output file ascii.sorted.bam does not exist" && exit 1
 
 echo ">>> Check if output is empty"
 [ ! -s "$test_dir/ascii.sorted.bam" ] \
-    && echo "Output file test_data/ascii.sorted.bam is empty" && exit 1
+    && echo "Output file ascii.sorted.bam is empty" && exit 1
 
 echo ">>> Check if output matches expected output"
 diff -a "$test_dir/ascii.sorted.bam.txt" "$out_dir/ascii_ref.sorted.txt" \
-    || (echo "Output file test_data/ascii.sorted.bam does not match expected output" && exit 1)
+    || (echo "Output file ascii.sorted.bam does not match expected output" && exit 1)
 
 rm "$test_dir/ascii.sorted.bam" "$test_dir/ascii.sorted.bam.txt"
 
@@ -60,15 +60,15 @@ echo ">>> Test 3: Sorting a BAM file with compression"
 
 echo ">>> Check if output file exists"
 [ ! -f "$test_dir/compressed.sorted.bam" ] \
-    && echo "Output file test_data/compressed.sorted.bam does not exist" && exit 1
+    && echo "Output file compressed.sorted.bam does not exist" && exit 1
 
 echo ">>> Check if output is empty"
 [ ! -s "$test_dir/compressed.sorted.bam" ] \
-    && echo "Output file test_data/compressed.sorted.bam is empty" && exit 1
+    && echo "Output file compressed.sorted.bam is empty" && exit 1
 
 echo ">>> Check if output matches expected output" #
 diff "$test_dir/compressed.sorted.bam.txt" "$out_dir/compressed_ref.sorted.txt" \
-    || (echo "Output file test_data/compressed.sorted.bam does not match expected output" && exit 1)
+    || (echo "Output file compressed.sorted.bam does not match expected output" && exit 1)
 
 rm "$test_dir/compressed.sorted.bam" "$test_dir/compressed.sorted.bam.txt"