nf-core_sarek/tests/test_annotation.yml at 4f6d0cc9150131c1c09c0e73e517d78eaa2e9c2f · maxulysse/nf-core_sarek · GitHub

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- name: Run snpEff
  command: nextflow run main.nf -profile test,annotation,docker --tools snpeff
  tags:
    - annotation
    - snpeff
  files:
    - path: results/annotation/test/test_snpEff.ann.vcf.gz
    - path: results/annotation/test/test_snpEff.ann.vcf.gz.tbi
    - path: results/multiqc
    - path: results/reports/snpeff/test/snpEff_summary.html
    - path: results/reports/snpeff/test/test_snpEff.csv
    - path: results/reports/snpeff/test/test_snpEff.genes.txt
- name: Run VEP
  command: nextflow run main.nf -profile test,annotation,docker --tools vep --skip_tools multiqc
  tags:
    - annotation
    - vep
  files:
    - path: results/annotation/test/test_VEP.ann.vcf.gz
    - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi
    - path: results/reports/EnsemblVEP/test/test_VEP.summary.html
- name: Run snpEff followed by VEP
  command: nextflow run main.nf -profile test,annotation,docker --tools merge --skip_tools multiqc
  tags:
    - annotation
    - merge
    - snpeff
    - vep
  files:
    - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz
    - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz.tbi
    - path: results/reports/EnsemblVEP/test/test_snpEff_VEP.summary.html
    - 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,docker --tools merge,snpeff,vep --skip_tools multiqc
  tags:
    - annotation
    - merge
    - snpeff
    - vep
  files:
    - path: results/annotation/test/test_VEP.ann.vcf.gz
    - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi
    - path: results/annotation/test/test_snpEff.ann.vcf.gz
    - path: results/annotation/test/test_snpEff.ann.vcf.gz.tbi
    - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz
    - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz.tbi
    - path: results/reports/EnsemblVEP/test/test_VEP.summary.html
    - path: results/reports/EnsemblVEP/test/test_snpEff_VEP.summary.html
    - path: results/reports/snpeff/test/snpEff_summary.html
    - path: results/reports/snpeff/test/test_snpEff.csv
    - path: results/reports/snpeff/test/test_snpEff.genes.txt
- name: Run VEP with fasta
  command: nextflow run main.nf -profile test,annotation,docker --tools vep --vep_include_fasta --skip_tools multiqc
  tags:
    - annotation
    - vep
  files:
    - path: results/annotation/test/test_VEP.ann.vcf.gz
    - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi
    - path: results/reports/EnsemblVEP/test/test_VEP.summary.html