- name: kraken2-test
  command: bash -c 'nextflow run ./subworkflows/local/kraken2/test.nf -entry test_kraken2 --wf kraken2 -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - kraken2
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/kraken2/nf-reports/kraken2-dag.dot
      contains: ['kraken2dag', 'KRAKEN2', 'versions']
    - path: bactopia/bactopia-runs/kraken2/nf-reports/kraken2-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/kraken2/nf-reports/kraken2-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/kraken2/nf-reports/kraken2-trace.txt
      contains: ['task_id']
    - path: bactopia/SRR2838702/tools/kraken2/SRR2838702.classified_1.fastq.gz
    - path: bactopia/SRR2838702/tools/kraken2/SRR2838702.classified_2.fastq.gz
    - path: bactopia/SRR2838702/tools/kraken2/SRR2838702.kraken2.report.txt
      contains: ['Enterobacteriaceae', 'Bacteria', 'unclassified']
    - path: bactopia/SRR2838702/tools/kraken2/SRR2838702.unclassified_1.fastq.gz
    - path: bactopia/SRR2838702/tools/kraken2/SRR2838702.unclassified_2.fastq.gz
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.err
      contains: ['Loading', 'classified', 'unclassified']
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.log
      contains: ['Loading', 'classified', 'unclassified']
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.out
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.sh
      contains: ['kraken2', 'END_VERSIONS']
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRR2838702/tools/kraken2/logs/versions.yml
      md5sum: 95cd3bacf8fa7d6f24cd6a539966ee3f

- name: kraken2-test-tarball
  command: bash -c 'nextflow run ./subworkflows/local/kraken2/test.nf -entry test_kraken2_tarball --wf kraken2 -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - kraken2
    - kraken2-tarball
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/kraken2/nf-reports/kraken2-dag.dot
      contains: ['kraken2dag', 'KRAKEN2', 'versions']
    - path: bactopia/bactopia-runs/kraken2/nf-reports/kraken2-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/kraken2/nf-reports/kraken2-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/kraken2/nf-reports/kraken2-trace.txt
      contains: ['task_id']
    - path: bactopia/SRR2838702/tools/kraken2/SRR2838702.classified_1.fastq.gz
    - path: bactopia/SRR2838702/tools/kraken2/SRR2838702.classified_2.fastq.gz
    - path: bactopia/SRR2838702/tools/kraken2/SRR2838702.kraken2.report.txt
      contains: ['Enterobacteriaceae', 'Bacteria', 'unclassified']
    - path: bactopia/SRR2838702/tools/kraken2/SRR2838702.unclassified_1.fastq.gz
    - path: bactopia/SRR2838702/tools/kraken2/SRR2838702.unclassified_2.fastq.gz
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.err
      contains: ['Loading', 'classified', 'unclassified']
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.log
      contains: ['Loading', 'classified', 'unclassified']
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.out
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.sh
      contains: ['kraken2', 'END_VERSIONS']
    - path: bactopia/SRR2838702/tools/kraken2/logs/nf-kraken2.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRR2838702/tools/kraken2/logs/versions.yml
      md5sum: a61f15dab97c2fb0374fc6156e0f446b
