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test_sentieon_joint_germline.yml
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test_sentieon_joint_germline.yml
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- name: Run joint germline variant calling with sentieon haplotyper
command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf
tags:
- germline
- sentieon_joint_germline
- variant_calling
- sentieon/haplotyper
files:
- path: results/csv/variantcalled.csv
md5sum: 6ec10f6455c2b5290c7f6fc687c529ca
- 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/sentieon_haplotyper/joint_variant_calling/joint_germline.bcftools_stats.txt
- path: results/reports/vcftools/sentieon_haplotyper/joint_variant_calling/joint_germline.FILTER.summary
- path: results/reports/vcftools/sentieon_haplotyper/joint_variant_calling/joint_germline.TsTv.count
- path: results/reports/vcftools/sentieon_haplotyper/joint_variant_calling/joint_germline.TsTv.qual
- path: results/variant_calling/sentieon_haplotyper/joint_variant_calling/joint_germline.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/sentieon_haplotyper/joint_variant_calling/joint_germline.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/variant_calling/sentieon_haplotyper/testN/testN.haplotyper.g.vcf.gz
- path: results/variant_calling/sentieon_haplotyper/testN/testN.haplotyper.g.vcf.gz.tbi
- path: results/variant_calling/sentieon_haplotyper/testT/testT.haplotyper.g.vcf.gz
- path: results/variant_calling/sentieon_haplotyper/testT/testT.haplotyper.g.vcf.gz.tbi
- path: results/haplotyper
should_exist: false
- name: Run joint germline variant calling with sentieon haplotyper all intervals at once
command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf --nucleotides_per_second 100
tags:
- germline
- sentieon_joint_germline
- variant_calling
- sentieon/haplotyper
files:
- path: results/csv/variantcalled.csv
md5sum: 6ec10f6455c2b5290c7f6fc687c529ca
- 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/sentieon_haplotyper/joint_variant_calling/joint_germline.bcftools_stats.txt
- path: results/reports/vcftools/sentieon_haplotyper/joint_variant_calling/joint_germline.FILTER.summary
- path: results/reports/vcftools/sentieon_haplotyper/joint_variant_calling/joint_germline.TsTv.count
- path: results/reports/vcftools/sentieon_haplotyper/joint_variant_calling/joint_germline.TsTv.qual
- path: results/variant_calling/sentieon_haplotyper/joint_variant_calling/joint_germline.vcf.gz
- path: results/variant_calling/sentieon_haplotyper/joint_variant_calling/joint_germline.vcf.gz.tbi
- path: results/variant_calling/sentieon_haplotyper/testN/testN.haplotyper.g.vcf.gz
- path: results/variant_calling/sentieon_haplotyper/testN/testN.haplotyper.g.vcf.gz.tbi
- path: results/variant_calling/sentieon_haplotyper/testT/testT.haplotyper.g.vcf.gz
- path: results/variant_calling/sentieon_haplotyper/testT/testT.haplotyper.g.vcf.gz.tbi
- path: results/haplotyper
should_exist: false
- name: Run joint germline variant calling with sentieon haplotyper with stub for VQSR
command: nextflow run main.nf -profile test_cache,software_license,tools_germline --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf -stub-run
tags:
- germline
- sentieon_joint_germline
- variant_calling
- vqsr
files:
- path: results/csv/variantcalled.csv
md5sum: 44415aaccc30c837943aea406c2f8d9d
- 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/sentieon_haplotyper/joint_variant_calling/joint_germline_recalibrated.bcftools_stats.txt
- path: results/reports/vcftools/sentieon_haplotyper/joint_variant_calling/joint_germline_recalibrated.FILTER.summary
- path: results/reports/vcftools/sentieon_haplotyper/joint_variant_calling/joint_germline_recalibrated.TsTv.count
- path: results/reports/vcftools/sentieon_haplotyper/joint_variant_calling/joint_germline_recalibrated.TsTv.qual
- path: results/variant_calling/sentieon_haplotyper/joint_variant_calling/joint_germline.vcf.gz
- path: results/variant_calling/sentieon_haplotyper/joint_variant_calling/joint_germline.vcf.gz.tbi
- path: results/variant_calling/sentieon_haplotyper/joint_variant_calling/joint_germline_recalibrated.vcf.gz
- path: results/variant_calling/sentieon_haplotyper/joint_variant_calling/joint_germline_recalibrated.vcf.gz.tbi
- path: results/variant_calling/sentieon_haplotyper/testN/testN.haplotyper.g.vcf.gz
- path: results/variant_calling/sentieon_haplotyper/testN/testN.haplotyper.g.vcf.gz.tbi
- path: results/variant_calling/sentieon_haplotyper/testT/testT.haplotyper.g.vcf.gz
- path: results/variant_calling/sentieon_haplotyper/testT/testT.haplotyper.g.vcf.gz.tbi
- path: results/haplotyper
should_exist: false