- name: bracken-test
  command: bash -c 'nextflow run ./subworkflows/local/bracken/test.nf -entry test_bracken --wf bracken -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - bracken
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/bracken/nf-reports/bracken-dag.dot
      contains: ['brackendag', 'BRACKEN', 'versions']
    - path: bactopia/bactopia-runs/bracken/nf-reports/bracken-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/bracken/nf-reports/bracken-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/bracken/nf-reports/bracken-trace.txt
      contains: ['task_id']
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.bracken.abundances.txt
      contains: ['Candidatus', 'Clostridium', 'kraken_assigned_reads']
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.bracken.adjusted.abundances.txt
      contains: ['Candidatus', 'Clostridium', 'kraken_assigned_reads']
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.bracken.krona.html
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.bracken.report.txt
      contains: ['Candidatus', 'Clostridium', 'root']
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.bracken.tsv
      contains: ['Candidatus', 'bracken_secondary_species_abundance', 'SRR2838702']
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.classified_1.fastq.gz
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.classified_2.fastq.gz
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.kraken2.krona.html
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.kraken2.report.txt
      contains: ['Candidatus', 'Clostridium', 'root']
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.unclassified_1.fastq.gz
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.unclassified_2.fastq.gz
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.err
      contains: ['sequences', 'classified', 'unclassified']
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.log
      contains: ['BRACKEN', 'species', 'complete']
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.out
      contains: ['BRACKEN', 'species', 'complete']
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.sh
      contains: ['kraken2', 'bracken', 'END_VERSIONS']
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRR2838702/tools/bracken/logs/versions.yml
      md5sum: 9bc7a68e6fd16c2dfe5f6eb0d687439f

- name: bracken-test-tarball
  command: bash -c 'nextflow run ./subworkflows/local/bracken/test.nf -entry test_bracken_tarball --wf bracken -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - bracken
    - bracken-tarball
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/bracken/nf-reports/bracken-dag.dot
      contains: ['brackendag', 'BRACKEN', 'versions']
    - path: bactopia/bactopia-runs/bracken/nf-reports/bracken-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/bracken/nf-reports/bracken-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/bracken/nf-reports/bracken-trace.txt
      contains: ['task_id']
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.bracken.abundances.txt
      contains: ['Candidatus', 'Clostridium', 'kraken_assigned_reads']
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.bracken.adjusted.abundances.txt
      contains: ['Candidatus', 'Clostridium', 'kraken_assigned_reads']
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.bracken.krona.html
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.bracken.report.txt
      contains: ['Candidatus', 'Clostridium', 'root']
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.bracken.tsv
      contains: ['Candidatus', 'bracken_secondary_species_abundance', 'SRR2838702']
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.classified_1.fastq.gz
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.classified_2.fastq.gz
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.kraken2.krona.html
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.kraken2.report.txt
      contains: ['Candidatus', 'Clostridium', 'root']
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.unclassified_1.fastq.gz
    - path: bactopia/SRR2838702/tools/bracken/SRR2838702.unclassified_2.fastq.gz
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.err
      contains: ['sequences', 'classified', 'unclassified']
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.log
      contains: ['BRACKEN', 'species', 'complete']
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.out
      contains: ['BRACKEN', 'species', 'complete']
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.sh
      contains: ['kraken2', 'bracken', 'END_VERSIONS']
    - path: bactopia/SRR2838702/tools/bracken/logs/nf-bracken.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRR2838702/tools/bracken/logs/versions.yml
      md5sum: dafd32420071ec6ea5b9df4866c5c7c0
