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test_prepare_recalibration_from_bam.yml
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- name: Run prepare_recalibration starting from bam
command: nextflow run main.nf -profile test,prepare_recalibration_bam
tags:
- input_bam
- prepare_recalibration
- preprocessing
files:
- path: results/csv/markduplicates.csv
md5sum: 90e2ab85d8af642d6548af448a9d4226
- path: results/csv/recalibrated.csv
md5sum: 1888a924bc70bd80165a96ad641e22d6
- path: results/multiqc
- path: results/preprocessing/converted/test/test.converted.cram
# binary changes md5sums on reruns.
- path: results/preprocessing/converted/test/test.converted.cram.crai
# binary changes md5sums on reruns.
- path: results/preprocessing/recal_table/test/test.recal.table
md5sum: 35d89a3811aa31711fc9815b6b80e6ec
- 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/mosdepth/test/test.recal.mosdepth.global.dist.txt
md5sum: bdb8f185c35dd1eec7ce2f69bce57972
- path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8
- path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
md5sum: 32ea70ef1b99def3dc900b4afd513a40
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz
md5sum: d034a60ae5c0768d67b9ba6442bd2212
- path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
md5sum: b3716e5cd1744610e69c29bd4ffad259
- path: results/reports/samtools/test/test.recal.cram.stats
# conda changes md5sums for test.
- path: results/preprocessing/mapped/
should_exist: false
- path: results/preprocessing/markduplicates/
should_exist: false
- name: Run prepare_recalibration starting from bam and skip baserecalibration
command: nextflow run main.nf -profile test,prepare_recalibration_bam,skip_bqsr --tools strelka
tags:
- input_bam
- prepare_recalibration
- preprocessing
files:
- path: results/csv/variantcalled.csv
md5sum: 4d0effd3d8dc2b814230a189e7ca9dba
- path: results/multiqc
- path: results/preprocessing/converted/test/test.converted.cram
# binary changes md5sums on reruns.
- path: results/preprocessing/converted/test/test.converted.cram.crai
# binary changes md5sums on reruns.
- path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt
# conda changes md5sums for test.
- path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary
md5sum: 39ff2cc8eb7495a14a6b76e0ab627027
- path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count
md5sum: ee7dafc8d941b8502a04a63dc3126fff
- path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual
# conda changes md5sums for test.
- path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
# binary changes md5sums on reruns.
- path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
# binary changes md5sums on reruns.
- path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
# binary changes md5sums on reruns.
- path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
# binary changes md5sums on reruns.
- path: results/csv/recalibrated.csv
should_exist: false
- path: results/preprocessing/recal_table/test/test.recal.table
should_exist: false
- 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/mosdepth
should_exist: false
- path: results/reports/samtools_stats
should_exist: false
- path: results/preprocessing/mapped/
should_exist: false
- path: results/preprocessing/markduplicates/
should_exist: false