test_alignment_to_fastq.yml

- name: Run alignment to fastq and then remap on bam files
  command: nextflow run main.nf -profile test,alignment_to_fastq --outdir results
  tags:
    - alignment_to_fastq
    - input_bam
  files:
    - path: results/csv/markduplicates.csv
      md5sum: 0d6120bb99e92f6810343270711ca53e
    - path: results/csv/markduplicates_no_table.csv
      md5sum: 2a2d3d4842befd4def39156463859ee3
    - path: results/csv/recalibrated.csv
      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
    - path: results/multiqc
    - path: results/preprocessing/markduplicates/test/test.md.cram
    # binary changes md5sums on reruns
    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
    # binary changes md5sums on reruns
    - path: results/preprocessing/recal_table/test/test.recal.table
      md5sum: 9c0517ffdc5d30a5c73b9f7df1ff3060
    - 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/fastqc/test-1
    - path: results/reports/markduplicates/test/test.md.cram.metrics
      contains: ["test	0	2820	2	2	0	828	0	0.293617	3807", "1.0	0.999986	1178	1178", "2.0	1.47674	800	800", "100.0	1.911145	0	0"]
    - 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
    # 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