From d247e10a0cbaaf9bfdd2f3169597c632a6c61f90 Mon Sep 17 00:00:00 2001 From: tefirman Date: Fri, 13 Dec 2024 11:21:18 -0800 Subject: [PATCH] Adding debugging to vc-test-run --- .../workflows/variant-calling-test-run.yml | 21 ++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/.github/workflows/variant-calling-test-run.yml b/.github/workflows/variant-calling-test-run.yml index 82efc3c..f932b9e 100644 --- a/.github/workflows/variant-calling-test-run.yml +++ b/.github/workflows/variant-calling-test-run.yml @@ -156,6 +156,21 @@ jobs: } EOF + # Add debugging for BQSR inputs + echo "=== Checking BQSR input files ===" + echo "dbSNP VCF:" + head -n 5 test/data/dbsnp.vcf + echo "Mills & 1000G VCF:" + zcat test/data/mills_1000G.vcf.gz | head -n 5 + echo "Known indels VCF:" + zcat test/data/known_indels.vcf.gz | head -n 5 + + # Validate VCF files + echo "=== Validating VCF files ===" + gatk ValidateVariants -V test/data/dbsnp.vcf -R test/data/ref.fasta + gatk ValidateVariants -V test/data/mills_1000G.vcf.gz -R test/data/ref.fasta + gatk ValidateVariants -V test/data/known_indels.vcf.gz -R test/data/ref.fasta + - name: Generate test BAM run: | # Create a more structured test BAM with multiple reads @@ -185,9 +200,13 @@ jobs: # Clean up intermediate files rm test/data/test.sam test/data/test.unsorted.bam + # Validate BAM file + echo "=== Validating BAM file ===" + gatk ValidateSamFile -I test/data/test.unmapped.bam + - name: Run test workflow run: | - java -jar cromwell-86.jar run variantCalling/variantCalling.wdl --inputs test/test-inputs.json + java -Xmx4g -jar cromwell-86.jar run variantCalling/variantCalling.wdl --inputs test/test-inputs.json - name: Check outputs run: |