nf-core_sarek/tests/test_bam_remap.yml at 7031b11236a8005b6b38f3eec7400fd991ddef50 · maxulysse/nf-core_sarek · GitHub

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- name: Run alignment to fastq and then remap on bam files
  command: nextflow run main.nf -profile test,alignment_to_fastq,docker
  tags:
    - alignment_to_fastq
  files:
    - path: results/cat/test-1_1.merged.fastq.gz
    - path: results/cat/test-1_2.merged.fastq.gz
    - path: results/collate/test-1.mapped_1.fq.gz
    - path: results/collate/test-1.mapped_2.fq.gz
    - path: results/collate/test-1.mapped_other.fq.gz
    - path: results/collate/test-1.mapped_singleton.fq.gz
    - path: results/collate/test-1.unmapped_1.fq.gz
    - path: results/collate/test-1.unmapped_2.fq.gz
    - path: results/collate/test-1.unmapped_other.fq.gz
    - path: results/collate/test-1.unmapped_singleton.fq.gz
    - 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/test-1
    - 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/samtools/test-1.bam
    - path: results/samtools/test-1.map_map.bam
    - path: results/samtools/test-1.map_unmap.bam
    - path: results/samtools/test-1.unmap_map.bam
    - path: results/samtools/test-1.unmap_unmap.bam