- name: ivar variants no gff no mpileup
  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff_no_mpileup -c tests/config/nextflow.config
  tags:
    - ivar
    - ivar_variants
  files:
    - path: output/ivar/test.tsv
      md5sum: 3fd376b8ad80f27a999edf3345d2014a
      
- name: ivar variants no gff with mpileup
  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c tests/config/nextflow.config --save_mpileup
  tags:
    - ivar
    - ivar_variants
  files:
    - path: output/ivar/test.tsv
      md5sum: 3fd376b8ad80f27a999edf3345d2014a
    - path: output/ivar/test.mpileup
      md5sum: b3dfd337dfcd313d6cc9680d7e796fe6

- name: ivar variants with gff with mpileup
  command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c tests/config/nextflow.config --gff tests/data/gff/sarscov2/MN908947.3.gff3 --save_mpileup
  tags:
    - ivar
    - ivar_variants
  files:
    - path: output/ivar/test.tsv
      md5sum: 3fd376b8ad80f27a999edf3345d2014a
    - path: output/ivar/test.mpileup
      md5sum: b3dfd337dfcd313d6cc9680d7e796fe6