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test_save_bam_mapped.yml
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test_save_bam_mapped.yml
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- name: Run save_bam_mapped
command: nextflow run main.nf -profile test,docker --save_bam_mapped
tags:
- preprocessing
- save_bam_mapped
files:
- path: results/csv/mapped.csv
- path: results/csv/markduplicates.csv
- path: results/csv/markduplicates_no_table.csv
- path: results/csv/recalibrated.csv
- path: results/multiqc
- path: results/preprocessing/mapped/test/test.bam
- path: results/preprocessing/mapped/test/test.bam.bai
- path: results/preprocessing/markduplicates/test/test.md.cram
- path: results/preprocessing/markduplicates/test/test.md.cram.crai
- path: results/preprocessing/recal_table/test/test.recal.table
- path: results/preprocessing/recalibrated/test/test.recal.cram
- path: results/preprocessing/recalibrated/test/test.recal.cram.crai
- path: results/reports/fastqc/test-test_L1
- 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/test/test.md.cram.stats
- path: results/reports/samtools/test/test.recal.cram.stats