sarek/tests/test_sentieon_dedup_from_cram.yml at 56c191642abdfea36d76a86ae41acbd328739a93 · nf-core/sarek · GitHub

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- name: Run sentieon dedup starting from CRAM
  command: nextflow run main.nf -profile test_cache,software_license,sentieon_dedup_cram --sentieon_extension --outdir results
  tags:
    - input_cram
    - preprocessing
    - sentieon/dedup
  files:
    - path: results/csv/markduplicates.csv
      md5sum: b06889d5be3ec1be6f5dd278ccc8f28e
    - path: results/csv/markduplicates_no_table.csv
      md5sum: 49661e56662d74f3a3db269387cbd9bf
    - path: results/csv/recalibrated.csv
      md5sum: 1888a924bc70bd80165a96ad641e22d6
    - path: results/multiqc
    - path: results/multiqc/multiqc_report.html
      contains: ["Sentieon Dedup Metrics", "PERCENT_DUPLICATION", "ESTIMATED_LIBRARY_SIZE"]
    - path: results/preprocessing/sentieon_dedup/test/test.dedup.cram
    # binary changes md5sums on reruns
    - path: results/preprocessing/sentieon_dedup/test/test.dedup.cram.crai
    # binary changes md5sums on reruns
    - path: results/preprocessing/recal_table/test/test.recal.table
      md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf
    - 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/sentieon_dedup/test/test.dedup.cram.metrics
      contains: ["testN	0	2820	2	2	0	828	0	0.293617	3807", "1.0	0.999986", "2.0	1.476740", "3.0	1.704038"]
    - path: results/reports/mosdepth/test/test.dedup.mosdepth.global.dist.txt
      md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5
    - path: results/reports/mosdepth/test/test.dedup.mosdepth.region.dist.txt
      md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
    - path: results/reports/mosdepth/test/test.dedup.mosdepth.summary.txt
      md5sum: b23cf96942b2ada3f41172a9349a1175
    - path: results/reports/mosdepth/test/test.dedup.regions.bed.gz
    # binary changes md5sums on reruns
    - path: results/reports/mosdepth/test/test.dedup.regions.bed.gz.csi
    # binary changes md5sums on reruns
    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
      md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5
    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
      md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
      md5sum: b23cf96942b2ada3f41172a9349a1175
    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
    # binary changes md5sums on reruns
    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
    # binary changes md5sums on reruns
    - path: results/reports/samtools/test/test.dedup.cram.stats
    # conda changes md5sums for test
    - path: results/reports/samtools/test/test.recal.cram.stats
    # conda changes md5sums for test
    - path: results/preprocessing/mapped/
      should_exist: false