sarek/tests/test_annotation.yml at 4f988332b5e5ce01d59d894393838931d4dd5072 · asp8200/sarek · GitHub

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- name: Run snpEff
  command: nextflow run main.nf -profile test,annotation --tools snpeff
  tags:
    - annotation
    - snpeff
  files:
    - path: results/annotation/test/test_snpEff.ann.vcf.gz
      md5sum: 01f24fdd76f73eefd695beea7b3d3d8e
    - path: results/annotation/test/test_snpEff.ann.vcf.gz.tbi
      md5sum: 51e418d9be9bb33f1d4123493b15b6c9
    - path: results/multiqc
    - path: results/reports/snpeff/test/snpEff_summary.html
      # snpEff_summary.html changes md5sums on reruns.
      contains: ["<b> Genome total length </b>", "<td> 100,286,402 </td>", "<td> MT192765.1 </td>"]
    - path: results/reports/snpeff/test/test_snpEff.csv
      # test_snpEff.csv changes md5sums on reruns.
      contains:
        [
          "Values , 50,100",
          "Count , 1,8",
          "Reference , 0",
          "Het , 1",
          "Hom , 8",
          "Missing , 0",
          "MT192765.1, Position,0,1",
          "MT192765.1,Count,0,0",
        ]
    - path: results/reports/snpeff/test/test_snpEff.genes.txt
      md5sum: 130536bf0237d7f3f746d32aaa32840a
- 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_snpEff.ann.vcf.gz</td></tr><tr><td>Output file</td><td>test_snpEff_VEP.ann.vcf</td></tr>",
          "General statistics",
          "Lines of input read",
          "Variants processed",
          "Variants filtered out",
          "Novel / existing variants",
          "Overlapped genes",
          "Overlapped transcripts",
          "Overlapped regulatory features",
        ]
- name: Run snpEff followed by VEP
  command: nextflow run main.nf -profile test,annotation --tools merge --skip_tools multiqc
  tags:
    - annotation
    - merge
    - snpeff
    - vep
  files:
    - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz
    # binary changes md5sums on reruns.
    - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz.tbi
      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
    - path: results/reports/EnsemblVEP/test/test_snpEff_VEP.summary.html
      # test_snpEff_VEP.summary.html changes md5sums on reruns.
      contains:
        [
          "<tr><td>Input file</td><td>test_snpEff.ann.vcf.gz</td></tr><tr><td>Output file</td><td>test_snpEff_VEP.ann.vcf</td></tr>",
          "General statistics",
          "Lines of input read",
          "Variants processed",
          "Variants filtered out",
          "Novel / existing variants",
          "Overlapped genes",
          "Overlapped transcripts",
          "Overlapped regulatory features",
        ]
    - path: results/annotation/test/test_snpEff.ann.vcf.gz
      should_exist: false
    - path: results/annotation/test/test_snpEff.ann.vcf.gz.tbi
      should_exist: false
    - path: results/annotation/test/test_VEP.ann.vcf.gz
      should_exist: false
    - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi
      should_exist: false
    - path: results/reports/snpeff/test/snpEff_summary.html
      should_exist: false
    - path: results/reports/snpeff/test/test_snpEff.csv
      should_exist: false
    - path: results/reports/snpeff/test/test_snpEff.genes.txt
      should_exist: false
    - path: results/reports/EnsemblVEP/test/test_VEP.summary.html
      should_exist: false
- name: Run snpEff, VEP and both consecutively
  command: nextflow run main.nf -profile test,annotation --tools merge,snpeff,vep --skip_tools multiqc
  tags:
    - annotation
    - merge
    - snpeff
    - 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/annotation/test/test_snpEff.ann.vcf.gz
      md5sum: 01f24fdd76f73eefd695beea7b3d3d8e
    - path: results/annotation/test/test_snpEff.ann.vcf.gz.tbi
      md5sum: 51e418d9be9bb33f1d4123493b15b6c9
    - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz
    # binary changes md5sums on reruns.
    - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz.tbi
      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
    - path: results/reports/EnsemblVEP/test/test_VEP.summary.html
    # text-based file changes md5sums on reruns.
    - path: results/reports/EnsemblVEP/test/test_snpEff_VEP.summary.html
    # text-based file changes md5sums on reruns.
    - path: results/reports/snpeff/test/snpEff_summary.html
    # text-based file changes md5sums on reruns.
    - path: results/reports/snpeff/test/test_snpEff.csv
    # text-based file changes md5sums on reruns.
    - path: results/reports/snpeff/test/test_snpEff.genes.txt
      md5sum: 130536bf0237d7f3f746d32aaa32840a
- 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.