- name: tbprofiler profile illumina
  command: nextflow run ./tests/modules/tbprofiler/profile -entry test_tbprofiler_profile_illumina -c ./tests/config/nextflow.config -c ./tests/modules/tbprofiler/profile/nextflow.config
  tags:
    - tbprofiler
    - tbprofiler/profile
  files:
    - path: output/tbprofiler/bam/test.bam
    - path: output/tbprofiler/results/test.results.json
      contains: ["genome_positions", "locus_tag", "tbprofiler_version"]
    - path: output/tbprofiler/vcf/test.targets.csq.vcf.gz

- name: tbprofiler profile nanopore
  command: nextflow run ./tests/modules/tbprofiler/profile -entry test_tbprofiler_profile_nanopore -c ./tests/config/nextflow.config -c ./tests/modules/tbprofiler/profile/nextflow.config
  tags:
    - tbprofiler
    - tbprofiler/profile
  files:
    - path: output/tbprofiler/bam/test.bam
    - path: output/tbprofiler/results/test.results.json
      contains: ["genome_positions", "locus_tag", "tbprofiler_version"]
    - path: output/tbprofiler/vcf/test.targets.csq.vcf.gz