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- name: Run default pipeline
command: nextflow run main.nf -profile test,docker
tags:
- default
- preprocessing
files:
- path: results/csv/markduplicates.csv
- path: results/csv/markduplicates_no_table.csv
- path: results/csv/recalibrated.csv
- path: results/multiqc
- path: results/preprocessing/test/markduplicates/test.md.cram
- path: results/preprocessing/test/markduplicates/test.md.cram.crai
- path: results/preprocessing/test/recal_table/test.recal.table
- path: results/preprocessing/test/recalibrated/test.recal.cram
- path: results/preprocessing/test/recalibrated/test.recal.cram.crai
- path: results/reports/fastqc
- path: results/reports/markduplicates/test/test.md.metrics
- 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_stats/test/test.md.cram.stats
- path: results/reports/samtools_stats/test/test.recal.cram.stats
- name: Run default pipeline without intervals
command: nextflow run main.nf -profile test,no_intervals,docker
tags:
- default
- no_intervals
- preprocessing
files:
- path: results/csv/markduplicates.csv
- path: results/csv/markduplicates_no_table.csv
- path: results/csv/recalibrated.csv
- path: results/multiqc
- path: results/no_intervals.bed
- path: results/no_intervals.bed.gz
- path: results/no_intervals.bed.gz.tbi
- path: results/preprocessing/test/markduplicates/test.md.cram
- path: results/preprocessing/test/markduplicates/test.md.cram.crai
- path: results/preprocessing/test/recal_table/test.recal.table
- path: results/preprocessing/test/recalibrated/test.recal.cram
- path: results/preprocessing/test/recalibrated/test.recal.cram.crai
- path: results/reports/fastqc
- path: results/reports/markduplicates/test/test.md.metrics
- 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_stats/test/test.md.cram.stats
- path: results/reports/samtools_stats/test/test.recal.cram.stats
- name: Run default pipeline with VC
command: nextflow run main.nf -profile test,docker --tools strelka
tags:
- default
- preprocessing
- variant_calling
- strelka
files:
- path: results/csv/markduplicates.csv
- path: results/csv/markduplicates_no_table.csv
- path: results/csv/recalibrated.csv
- path: results/csv/variantcalled.csv
- path: results/multiqc
- path: results/preprocessing/test/markduplicates/test.md.cram
- path: results/preprocessing/test/markduplicates/test.md.cram.crai
- path: results/preprocessing/test/recal_table/test.recal.table
- path: results/preprocessing/test/recalibrated/test.recal.cram
- path: results/preprocessing/test/recalibrated/test.recal.cram.crai
- path: results/reports/bcftools/test/strelka/test.strelka.variants.bcftools_stats.txt
- path: results/reports/fastqc
- path: results/reports/markduplicates/test/test.md.metrics
- 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_stats/test/test.md.cram.stats
- path: results/reports/samtools_stats/test/test.recal.cram.stats
- path: results/reports/vcftools/test/strelka/test.strelka.variants.FILTER.summary
- path: results/reports/vcftools/test/strelka/test.strelka.variants.TsTv.count
- path: results/reports/vcftools/test/strelka/test.strelka.variants.TsTv.qual
- path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz
- path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi
- path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz
- path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi