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test_freebayes.yml
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- name: Run variant calling on germline sample with freebayes
command: nextflow run main.nf -profile test,targeted --tools freebayes --outdir results
tags:
- freebayes
- germline
- variant_calling
files:
- path: results/csv/markduplicates.csv
md5sum: 0d6120bb99e92f6810343270711ca53e
- path: results/csv/markduplicates_no_table.csv
md5sum: 2a2d3d4842befd4def39156463859ee3
- path: results/csv/recalibrated.csv
md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
- path: results/csv/variantcalled.csv
md5sum: 0cc6a67fedb2ef9ce97e463d310f9f30
- path: results/multiqc
- path: results/preprocessing/markduplicates/test/test.md.cram
# binary changes md5sums on reruns
- path: results/preprocessing/markduplicates/test/test.md.cram.crai
# binary changes md5sums on reruns
- path: results/preprocessing/recal_table/test/test.recal.table
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.cram
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns
- path: results/reports/bcftools/freebayes/test/test.freebayes.bcftools_stats.txt
# conda changes md5sums for test
- path: results/reports/fastqc/test-test_L1
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- 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.per-base.bed.gz
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- 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.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary
md5sum: 75824ce08910acce7e9f6adb4d635850
- path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count
md5sum: 3c198f7ec7fe2f5d365218ba0ff64197
- path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual
- path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/freebayes
should_exist: false
- name: Run variant calling on germline sample with freebayes without intervals
command: nextflow run main.nf -profile test --tools freebayes --no_intervals --outdir results
tags:
- freebayes
- germline
- no_intervals
- variant_calling
files:
- path: results/csv/markduplicates.csv
md5sum: 0d6120bb99e92f6810343270711ca53e
- path: results/csv/markduplicates_no_table.csv
md5sum: 2a2d3d4842befd4def39156463859ee3
- path: results/csv/recalibrated.csv
md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
- path: results/csv/variantcalled.csv
md5sum: 0cc6a67fedb2ef9ce97e463d310f9f30
- 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/preprocessing/markduplicates/test/test.md.cram
# binary changes md5sums on reruns
- path: results/preprocessing/markduplicates/test/test.md.cram.crai
# binary changes md5sums on reruns
- path: results/preprocessing/recal_table/test/test.recal.table
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.cram
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns
- path: results/reports/bcftools/freebayes/test/test.freebayes.bcftools_stats.txt
# conda changes md5sums for test
- path: results/reports/fastqc/test-test_L1
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- 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.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary
md5sum: 562eaa4512cd4b57e6cfca7b44957d1c
- path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count
md5sum: 4e6935b1e1906e57be1b54c0dffe7169
- path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual
- path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/freebayes
should_exist: false
- name: Run variant calling on somatic sample with freebayes
command: nextflow run main.nf -profile test,pair,targeted --tools freebayes --outdir results
tags:
- freebayes
- somatic
- variant_calling
files:
- path: results/csv/markduplicates.csv
md5sum: e8e587ac25253ff7ab8f1cc66d410c98
- path: results/csv/markduplicates_no_table.csv
md5sum: 617574c9b607e5daaf4ad56d48982247
- path: results/csv/recalibrated.csv
md5sum: 008dff17e2a0d96ef9c1cae12fcab6ab
- path: results/csv/variantcalled.csv
md5sum: b31f56256a1cfa839a2ea7f7ba6c1c45
- path: results/multiqc
- path: results/preprocessing/markduplicates/test/test.md.cram
# binary changes md5sums on reruns
- path: results/preprocessing/markduplicates/test/test.md.cram.crai
# binary changes md5sums on reruns
- path: results/preprocessing/markduplicates/test2/test2.md.cram
# binary changes md5sums on reruns
- path: results/preprocessing/markduplicates/test2/test2.md.cram.crai
# binary changes md5sums on reruns
- path: results/preprocessing/recal_table/test/test.recal.table
md5sum: c990e4f1b7dbd5a3a623882a54ae2bf2
- path: results/preprocessing/recal_table/test2/test2.recal.table
md5sum: 00d6877d68d622d81e4d633c4e340e7e
- path: results/preprocessing/recalibrated/test/test.recal.cram
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test2/test2.recal.cram
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai
# binary changes md5sums on reruns
- path: results/reports/bcftools/freebayes/test/test.freebayes.bcftools_stats.txt
# conda changes md5sums for test
- path: results/reports/bcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.bcftools_stats.txt
# conda changes md5sums for test
- path: results/reports/fastqc/test-test_L1
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"]
- path: results/reports/markduplicates/test2/test2.md.cram.metrics
contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi
- path: results/reports/mosdepth/test/test.md.regions.bed.gz
- path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
- 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.per-base.bed.gz
- path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
- path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt
- path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
- path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz
- path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz.csi
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz
- path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz
- path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz
- path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test2/test2.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test2/test2.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary
md5sum: 43d53e36cbb1091f915b2499e545b41e
- path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count
md5sum: 650f3dc78c5aaaecfe8ffa3d499e812f
- path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual
- path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.FILTER.summary
md5sum: 84039d55edf0981d6b9b81252aff6741
- path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.TsTv.count
md5sum: 6c6038d43eb7fa766909b495979d120e
- path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.TsTv.qual
# the text-based file test2_vs_test.freebayes.TsTv.qual seemingly changes content on reruns!
- path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/freebayes
should_exist: false
- name: Run variant calling on somatic sample with freebayes without intervals
command: nextflow run main.nf -profile test,pair,targeted --tools freebayes --no_intervals --outdir results
tags:
- freebayes
- somatic
- no_intervals
- variant_calling
files:
- path: results/csv/markduplicates.csv
md5sum: e8e587ac25253ff7ab8f1cc66d410c98
- path: results/csv/markduplicates_no_table.csv
md5sum: 617574c9b607e5daaf4ad56d48982247
- path: results/csv/recalibrated.csv
md5sum: 008dff17e2a0d96ef9c1cae12fcab6ab
- path: results/csv/variantcalled.csv
md5sum: b31f56256a1cfa839a2ea7f7ba6c1c45
- 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/preprocessing/markduplicates/test/test.md.cram
# binary changes md5sums on reruns
- path: results/preprocessing/markduplicates/test/test.md.cram.crai
# binary changes md5sums on reruns
- path: results/preprocessing/markduplicates/test2/test2.md.cram
# binary changes md5sums on reruns
- path: results/preprocessing/markduplicates/test2/test2.md.cram.crai
# binary changes md5sums on reruns
- path: results/preprocessing/recal_table/test/test.recal.table
md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
- path: results/preprocessing/recal_table/test2/test2.recal.table
md5sum: 0626cd4337eab79b38b5bc5c95e0c003
- path: results/preprocessing/recalibrated/test/test.recal.cram
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test2/test2.recal.cram
# binary changes md5sums on reruns
- path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai
# binary changes md5sums on reruns
- path: results/reports/bcftools/freebayes/test/test.freebayes.bcftools_stats.txt
# conda changes md5sums for test
- path: results/reports/bcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.bcftools_stats.txt
# conda changes md5sums for test
- path: results/reports/fastqc/test-test_L1
- path: results/reports/markduplicates/test/test.md.cram.metrics
contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"]
- path: results/reports/markduplicates/test2/test2.md.cram.metrics
contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"]
- path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz
- path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi
- 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/mosdepth/test2/test2.md.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
- path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz
- path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz.csi
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
- path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
- path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz
- path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi
- path: results/reports/samtools/test/test.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test2/test2.md.cram.stats
# conda changes md5sums for test
- path: results/reports/samtools/test2/test2.recal.cram.stats
# conda changes md5sums for test
- path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary
md5sum: 76c5919541536c12b5c8a6094d6d78d5
- path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count
md5sum: 0a0464beef110bc0f3c5a35d022b528e
- path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual
- path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.FILTER.summary
md5sum: d2d717fef7c18ef9b40bbbc5c5bbf101
- path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.TsTv.count
md5sum: e09dacc71bf72254e3aace1cc7c1e16d
- path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.TsTv.qual
# the text-based file test2_vs_test.freebayes.TsTv.qual seemingly changes content on reruns!
- path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/freebayes
should_exist: false
- name: Run variant calling on tumor_only sample with freebayes
command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes --outdir results
tags:
- freebayes
- tumor_only
- variant_calling
files:
- path: results/csv/variantcalled.csv
md5sum: 5c5938a7bcc814cdaf5433c1120964c5
- path: results/multiqc
- path: results/reports/bcftools/freebayes/sample2/sample2.freebayes.bcftools_stats.txt
# conda changes md5sums for test
- path: results/reports/vcftools/freebayes/sample2/sample2.freebayes.FILTER.summary
md5sum: 0df3ddeec5779344b5d463347c9c6ea8
- path: results/reports/vcftools/freebayes/sample2/sample2.freebayes.TsTv.count
md5sum: b1d308ed5087361a584cb61e7b835e1e
- path: results/reports/vcftools/freebayes/sample2/sample2.freebayes.TsTv.qual
# content changes md5sums on reruns
- path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/freebayes
should_exist: false
- name: Run variant calling on tumor_only sample with freebayes without intervals
command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes --no_intervals --outdir results
tags:
- freebayes
- no_intervals
- tumor_only
- variant_calling
files:
- path: results/csv/variantcalled.csv
md5sum: 5c5938a7bcc814cdaf5433c1120964c5
- path: results/multiqc
- path: results/reports/bcftools/freebayes/sample2/sample2.freebayes.bcftools_stats.txt
# conda changes md5sums for test
- path: results/reports/vcftools/freebayes/sample2/sample2.freebayes.FILTER.summary
md5sum: ee513ecf779b6e201b8ef98f95f25aab
- path: results/reports/vcftools/freebayes/sample2/sample2.freebayes.TsTv.count
md5sum: 2dc153ad5af26c9f8aa82442bf65b4bf
- path: results/reports/vcftools/freebayes/sample2/sample2.freebayes.TsTv.qual
# content changes md5sums on reruns
- path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz
# binary changes md5sums on reruns
- path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi
# binary changes md5sums on reruns
- path: results/freebayes
should_exist: false