From a3bf92cef5b808f639a45b32f79e0847efe0b565 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Sat, 5 Aug 2023 17:26:48 +0000 Subject: [PATCH] add tests for gvcf when one interval group --- tests/test_joint_germline.yml | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/tests/test_joint_germline.yml b/tests/test_joint_germline.yml index 45dc2b06f0..d4ba188134 100644 --- a/tests/test_joint_germline.yml +++ b/tests/test_joint_germline.yml @@ -30,3 +30,35 @@ - path: results/variant_calling/haplotypecaller/testT/testT.haplotypecaller.g.vcf.gz.tbi - path: results/haplotypecaller should_exist: false +- name: Run joint germline variant calling with haplotypecaller all intervals at once + command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --nucleotides_per_second 100 + tags: + - germline + - joint_germline + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: d2dffdbd2b4f1f26a06637592d24dab3 + - path: results/multiqc + - path: results/preprocessing/recalibrated/test/test.recal.cram + should_exist: false + - path: results/preprocessing/recalibrated/test/test.recal.cram.crai + should_exist: false + - path: results/reports/bcftools/haplotypecaller/joint_variant_calling/joint_germline.bcftools_stats.txt + # Not stable enough + - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.FILTER.summary + # Not stable enough + - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.count + # Not stable enough + - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.qual + # Not stable enough + - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz + # binary changes md5sums on reruns + - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz.tbi + # binary changes md5sums on reruns + - path: results/variant_calling/haplotypecaller/testN/testN.haplotypecaller.g.vcf.gz + - path: results/variant_calling/haplotypecaller/testN/testN.haplotypecaller.g.vcf.gz.tbi + - path: results/variant_calling/haplotypecaller/testT/testT.haplotypecaller.g.vcf.gz + - path: results/variant_calling/haplotypecaller/testT/testT.haplotypecaller.g.vcf.gz.tbi + - path: results/haplotypecaller + should_exist: false