- name: kraken2 run single-end
  command: nextflow run ./tests/software/kraken2/run -entry test_kraken2_run_single_end -c tests/config/nextflow.config
  tags:
    - kraken2
    - kraken2_run
    - kraken2_run_single_end
  files:
    - path: output/kraken2/test.classified.fastq.gz
      should_exist: true
    - path: output/kraken2/test.unclassified.fastq.gz
      should_exist: true
    - path: output/kraken2/test.kraken2.report.txt
      md5sum: 4227755fe40478b8d7dc8634b489761e

- name: kraken2 run paired-end
  command: nextflow run ./tests/software/kraken2/run -entry test_kraken2_run_paired_end -c tests/config/nextflow.config
  tags:
    - kraken2
    - kraken2_run
    - kraken2_run_paired_end
  files:
    - path: output/kraken2/test.classified_1.fastq.gz
      should_exist: true
    - path: output/kraken2/test.classified_2.fastq.gz
      should_exist: true
    - path: output/kraken2/test.unclassified_1.fastq.gz
      should_exist: true
    - path: output/kraken2/test.unclassified_2.fastq.gz
      should_exist: true
    - path: output/kraken2/test.kraken2.report.txt
      md5sum: 5fb165fd0bdf920ff6cf6f734371a4cf