test_annotation_vep.yml

- name: Run VEP
  command: nextflow run main.nf -profile test,annotation --tools vep --skip_tools multiqc
  tags:
    - annotation
    - vep
  files:
    - path: results/annotation/test/test_VEP.ann.vcf.gz
    # binary changes md5sums on reruns.
    - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi
      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
    - path: results/reports/EnsemblVEP/test/test_VEP.summary.html
      # test_VEP.summary.html changes md5sums on reruns.
      contains:
        ["<tr><td>Input file</td><td>test.vcf.gz</td></tr><tr><td>Output file</td><td>test_VEP.ann.vcf</td></tr>"]
- name: Run VEP with fasta
  command: nextflow run main.nf -profile test,annotation --tools vep --vep_include_fasta --skip_tools multiqc
  tags:
    - annotation
    - vep
  files:
    - path: results/annotation/test/test_VEP.ann.vcf.gz
    # binary changes md5sums on reruns.
    - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi
      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
    - path: results/reports/EnsemblVEP/test/test_VEP.summary.html
      # text-based file changes md5sums on reruns.
      contains:
        ["<tr><td>Input file</td><td>test.vcf.gz</td></tr><tr><td>Output file</td><td>test_VEP.ann.vcf</td></tr>"]