Consolidating steps in vc-test-run

.github/workflows/variant-calling-test-run.yml

@@ -198,13 +198,8 @@ jobs:
           gatk ValidateVariants -V mills_1000G.vcf.gz -R ref.fasta
           gatk ValidateVariants -V known_indels.vcf.gz -R ref.fasta
 
-          # Navigating back to original directory
-          cd ../../
-
-      - name: Generate test BAM
-        run: |
           # Create a test BAM with unmapped reads
-          cat << EOF > test/data/test.sam
+          cat << EOF > test.sam
           @HD	VN:1.6	SO:queryname
           @SQ	SN:chr20	LN:63025520
           @RG	ID:test	SM:test_sample	PL:ILLUMINA	LB:lib1	PU:unit1
@@ -217,21 +212,24 @@ jobs:
           EOF
           
           # Convert SAM to BAM and proper sorting
-          samtools view -b test/data/test.sam > test/data/test.unsorted.bam
-          samtools sort -n test/data/test.unsorted.bam > test/data/test.unmapped.bam
+          samtools view -b test.sam > test.unsorted.bam
+          samtools sort -n test.unsorted.bam > test.unmapped.bam
           
           # Debug: Check the BAM
           echo "=== Checking final BAM structure ==="
-          samtools view -H test/data/test.unmapped.bam
+          samtools view -H test.unmapped.bam
           echo "=== First few reads ==="
-          samtools view test/data/test.unmapped.bam | head -n 2
+          samtools view test.unmapped.bam | head -n 2
           
           # Clean up intermediate files
-          rm test/data/test.sam test/data/test.unsorted.bam
+          rm test.sam test.unsorted.bam
 
           # Validate BAM file
           echo "=== Validating BAM file ==="
-          gatk ValidateSamFile -I test/data/test.unmapped.bam
+          gatk ValidateSamFile -I test.unmapped.bam
+
+          # Navigating back to original directory
+          cd ../../
 
       - name: Run test workflow
         run: |