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maxulysse committed Oct 3, 2024
1 parent edd0624 commit 08be956
Showing 1 changed file with 27 additions and 50 deletions.
77 changes: 27 additions & 50 deletions tests/test_deepvariant.yml
Original file line number Diff line number Diff line change
@@ -6,30 +6,20 @@
- variant_calling
files:
- path: results/multiqc
- path: results/reports/bcftools/deepvariant/sample1/sample1.deepvariant.bcftools_stats.txt
# md5sum: a6634ceb1c712de14009b05d273713a7
- path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.FILTER.summary
md5sum: acce7a163f4070226429f9d6bc3fbd2c
- path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.TsTv.count
md5sum: de1632b8413f4c14c78acdc2df5c5224
- path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.TsTv.qual
md5sum: a9c05f0ecb0bb71123e345589bd7089c
- path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/deepvariant
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
- path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
- path: results/reports/bcftools/deepvariant/test/test.deepvariant.bcftools_stats.txt
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- path: results/reports/samtools/test/test.recal.cram.stats
- path: results/reports/vcftools/deepvariant/test/test.deepvariant.FILTER.summary
- path: results/reports/vcftools/deepvariant/test/test.deepvariant.TsTv.count
- path: results/reports/vcftools/deepvariant/test/test.deepvariant.TsTv.qual
- path: results/variant_calling/deepvariant/test/test.deepvariant.g.vcf.gz
- path: results/variant_calling/deepvariant/test/test.deepvariant.g.vcf.gz.tbi
- path: results/variant_calling/deepvariant/test/test.deepvariant.vcf.gz
- path: results/variant_calling/deepvariant/test/test.deepvariant.vcf.gz.tbi
- name: Run variant calling on germline sample with deepvariant without intervals
command: nextflow run main.nf -profile test,tools_germline_deepvariant --tools deepvariant --no_intervals --outdir results
tags:
@@ -40,31 +30,18 @@
files:
- path: results/multiqc
- path: results/no_intervals.bed
md5sum: f3dac01ea66b95fe477446fde2d31489
- path: results/no_intervals.bed.gz
md5sum: f3dac01ea66b95fe477446fde2d31489
- path: results/no_intervals.bed.gz.tbi
md5sum: f3dac01ea66b95fe477446fde2d31489
- path: results/reports/bcftools/deepvariant/sample1/sample1.deepvariant.bcftools_stats.txt
# md5sum: 0c48d8e315ca23c5dc2e7bf71ea0b6a6
- path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.FILTER.summary
md5sum: 7b17bd18c2d4bf129561c7c6a419a889
- path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.TsTv.count
md5sum: e570b07835a793bbab4f517cabed5a45
- path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.TsTv.qual
md5sum: 03f64b8092fc212bcb746b08f9e676a5
- path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/deepvariant
should_exist: false
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
- path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz
- path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi
- path: results/reports/samtools/sample1/sample1.recal.cram.stats
- path: results/reports/bcftools/deepvariant/test/test.deepvariant.bcftools_stats.txt
- path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- path: results/reports/samtools/test/test.recal.cram.stats
- path: results/reports/vcftools/deepvariant/test/test.deepvariant.FILTER.summary
- path: results/reports/vcftools/deepvariant/test/test.deepvariant.TsTv.count
- path: results/reports/vcftools/deepvariant/test/test.deepvariant.TsTv.qual
- path: results/variant_calling/deepvariant/test/test.deepvariant.g.vcf.gz
- path: results/variant_calling/deepvariant/test/test.deepvariant.g.vcf.gz.tbi
- path: results/variant_calling/deepvariant/test/test.deepvariant.vcf.gz
- path: results/variant_calling/deepvariant/test/test.deepvariant.vcf.gz.tbi

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