test_annotation.yml

- name: Run snpEff
  command: nextflow run main.nf -profile test,docker --annotate_tools snpeff --outdir results --download_cache
  tags:
    - annotation
    - snpeff
  files:
    - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff.ann.vcf.gz
    - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff.ann.vcf.gz.tbi
    - path: results/reports/multiqc_report.html
- name: Run VEP
  command: nextflow run main.nf -profile test,docker --annotate_tools vep --skip_multiqc --outdir results --download_cache
  tags:
    - annotation
    - vep
  files:
    - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_VEP.ann.vcf.gz
    - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_VEP.ann.vcf.gz.tbi
- name: Run snpEff followed by VEP
  command: nextflow run main.nf -profile test,docker --annotate_tools merge --skip_multiqc --outdir results --download_cache
  tags:
    - annotation
    - merge
    - snpeff
    - vep
  files:
    - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff_VEP.ann.vcf.gz
    - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff_VEP.ann.vcf.gz.tbi