- name: snippy run test_snippy_run
  command: |
    nextflow run tests/modules/snippy/run -entry test_snippy_run -c tests/config/nextflow.config -c tests/modules/snippy/run/nextflow.config
  tags:
    - snippy/run
    - snippy
  files:
    - path: output/snippy/test/test.aligned.fa
      md5sum: 47e3390d4167edf1955d162d37aca5e3
    - path: output/snippy/test/test.bam
    - path: output/snippy/test/test.bam.bai
    - path: output/snippy/test/test.bed
    - path: output/snippy/test/test.consensus.fa
      md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
    - path: output/snippy/test/test.consensus.subs.fa
      md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
    - path: output/snippy/test/test.csv
      md5sum: 322f942115e5945c2041a88246166703
    - path: output/snippy/test/test.filt.vcf
      contains: ["fileformat", "freebayes", "CHROM"]
    - path: output/snippy/test/test.gff
      md5sum: df19e1b84ba6f691d20c72b397c88abf
    - path: output/snippy/test/test.html
      md5sum: 1ccbf0ffcadae1a6b2e11681d24c9938
    - path: output/snippy/test/test.log
      contains: ["snippy", "consensus", "subs"]
    - path: output/snippy/test/test.raw.vcf
      contains: ["fileformat", "freebayes", "CHROM"]
    - path: output/snippy/test/test.tab
      md5sum: beb9bde3bce985e53e8feba9ec5b136e
    - path: output/snippy/test/test.txt
      contains: ["DateTime", "ReadFiles", "VariantTotal"]
    - path: output/snippy/test/test.vcf
      contains: ["fileformat", "freebayes", "CHROM"]
    - path: output/snippy/test/test.vcf.gz
    - path: output/snippy/test/test.vcf.gz.csi
      md5sum: bed9fa291c220a1ba04eb2d448932ffc
    - path: output/snippy/versions.yml
      md5sum: 518aad56c4dbefb6cbcde5ab38cf7b5d