- name: merlin-test
  command: bash -c 'nextflow run ./subworkflows/local/merlin/test.nf -entry test_merlin --wf merlin -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - merlin
    - bactopia-tools
  files:
    - path: bactopia/GCF_000017085/tools/agrvate/GCF_000017085-agr_gp.tab
      md5sum: 04031d5b20fabcc4b3ddeef707e94029
    - path: bactopia/GCF_000017085/tools/agrvate/GCF_000017085-blastn_log.txt
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/agrvate/GCF_000017085-summary.tab
      md5sum: b483a3d6ca1908ab813427b06751e51a
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.err
      contains: ['download', 'usearch', 'mummer']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.log
      contains: ['agr', 'Processing']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.out
      contains: ['agr', 'Processing']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.sh
      contains: ['agrvate', 'END_VERSIONS']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/nf-agrvate.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000017085/tools/agrvate/logs/versions.yml
      md5sum: 0d1b1a5e5fdfb3ad02a7fc8164743428
    - path: bactopia/GCF_000017085/tools/mashdist/merlin/GCF_000017085-dist.txt
      md5sum: c8d438cb4798c2bc324dc525bc38a69f
    - path: bactopia/GCF_000017085/tools/mashdist/merlin/logs/nf-mashdist.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/mashdist/merlin/logs/nf-mashdist.err
      contains: ['Estimated', 'coverage']
    - path: bactopia/GCF_000017085/tools/mashdist/merlin/logs/nf-mashdist.log
      contains: ['Estimated', 'coverage']
    - path: bactopia/GCF_000017085/tools/mashdist/merlin/logs/nf-mashdist.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/mashdist/merlin/logs/nf-mashdist.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000017085/tools/mashdist/merlin/logs/nf-mashdist.sh
      contains: ['mash', 'END_VERSIONS']
    - path: bactopia/GCF_000017085/tools/mashdist/merlin/logs/nf-mashdist.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000017085/tools/mashdist/merlin/logs/versions.yml
      md5sum: 12395d11242d9c1ffb0acdba7a871c0e
    - path: bactopia/GCF_000017085/tools/spatyper/GCF_000017085.tsv
      md5sum: 6afe7a90c591e32107d86c0e81029f54
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.err
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.log
      contains: ['Start', 'Repeats', 'Results']
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.out
      contains: ['Start', 'Repeats', 'Results']
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.sh
      contains: ['spaTyper', 'END_VERSIONS']
    - path: bactopia/GCF_000017085/tools/spatyper/logs/nf-spatyper.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000017085/tools/spatyper/logs/versions.yml
      md5sum: 85b827cfeaa814eebb2519bfbbffc090
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/GCF_000017085.tsv
      md5sum: 718ce0a77a9edd79c639b2c8e61aded9
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.err
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.log
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.out
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.sh
      contains: ['sccmec', 'END_VERSIONS']
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/nf-staphopiasccmec.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000017085/tools/staphopiasccmec/logs/versions.yml
      md5sum: 46ea307e20d99b14cf6055ccc71aa7af
    - path: bactopia/bactopia-runs/merlin/merged-results/agrvate.tsv
      contains: ['agr_group', 'GCF_000017085']
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/agrvate-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/agrvate-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/agrvate-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/agrvate-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/agrvate-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/agrvate-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/agrvate-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/agrvate-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/spatyper-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/spatyper-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/spatyper-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/spatyper-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/spatyper-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/spatyper-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/spatyper-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/spatyper-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/staphopiasccmec-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/staphopiasccmec-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/staphopiasccmec-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/staphopiasccmec-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/staphopiasccmec-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/staphopiasccmec-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/staphopiasccmec-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/merlin/merged-results/logs/staphopiasccmec-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/merlin/merged-results/spatyper.tsv
      md5sum: 6afe7a90c591e32107d86c0e81029f54
    - path: bactopia/bactopia-runs/merlin/merged-results/staphopiasccmec.tsv
      md5sum: 09c32087d2d3c4613926c1762b21e5ec
    - path: bactopia/bactopia-runs/merlin/nf-reports/merlin-dag.dot
      contains: ['merlindag', 'MERLIN', 'versions']
    - path: bactopia/bactopia-runs/merlin/nf-reports/merlin-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/merlin/nf-reports/merlin-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/merlin/nf-reports/merlin-trace.txt
      contains: ['task_id']

- name: merlin-full_test
  command: bash -c 'nextflow run ./subworkflows/local/merlin/test.nf -entry test_merlinfull --wf merlin --full_merlin -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - merlin-full
    - bactopia-tools
  files:
    - path: bactopia/GCF_000292685/tools/agrvate/GCF_000292685-agr_gp.tab
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/agrvate/GCF_000292685-blastn_log.txt
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/agrvate/GCF_000292685-hmm-log.txt
      contains: ['HMMER', 'ok']
    - path: bactopia/GCF_000292685/tools/agrvate/GCF_000292685-hmm.tab
      contains: ['nhmmer', 'ok']
    - path: bactopia/GCF_000292685/tools/agrvate/GCF_000292685-summary.tab
      md5sum: cc92552b9c42ebc732584bb6a30aee96
    - path: bactopia/GCF_000292685/tools/agrvate/logs/nf-agrvate.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/agrvate/logs/nf-agrvate.err
      contains: ['download', 'usearch', 'mummer']
    - path: bactopia/GCF_000292685/tools/agrvate/logs/nf-agrvate.log
      contains: ['agr', 'Processing']
    - path: bactopia/GCF_000292685/tools/agrvate/logs/nf-agrvate.out
      contains: ['agr', 'Processing']
    - path: bactopia/GCF_000292685/tools/agrvate/logs/nf-agrvate.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/agrvate/logs/nf-agrvate.sh
      contains: ['agrvate', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/agrvate/logs/nf-agrvate.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/agrvate/logs/versions.yml
      md5sum: 9ecfbcfdf7cd13eec1fa3485fb79558b
    - path: bactopia/GCF_000292685/tools/ectyper/GCF_000292685.tsv
      md5sum: a8e6673164ac13e84b42ab690a2721da
    - path: bactopia/GCF_000292685/tools/ectyper/blast_output_alleles.txt
      md5sum: 27f3f5e84f7da451b2948d61589cdb06
    - path: bactopia/GCF_000292685/tools/ectyper/logs/ectyper.log
      contains: ['Gathering', 'Serotype', 'successfully']
    - path: bactopia/GCF_000292685/tools/ectyper/logs/nf-ectyper.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/ectyper/logs/nf-ectyper.err
      contains: ['ectyper', 'INFO', 'successfully']
    - path: bactopia/GCF_000292685/tools/ectyper/logs/nf-ectyper.log
      contains: ['ectyper', 'INFO', 'successfully']
    - path: bactopia/GCF_000292685/tools/ectyper/logs/nf-ectyper.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/ectyper/logs/nf-ectyper.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/ectyper/logs/nf-ectyper.sh
      contains: ['ectyper', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/ectyper/logs/nf-ectyper.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/ectyper/logs/versions.yml
      md5sum: eb37a2a9b73e312a306e198975dedd8c
    - path: bactopia/GCF_000292685/tools/emmtyper/GCF_000292685.tsv
      md5sum: 6b638803cd53f64c61b706966e05d321
    - path: bactopia/GCF_000292685/tools/emmtyper/logs/nf-emmtyper.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/emmtyper/logs/nf-emmtyper.err
      contains: ['emmtyper', 'Finished']
    - path: bactopia/GCF_000292685/tools/emmtyper/logs/nf-emmtyper.log
      contains: ['emmtyper', 'Finished']
    - path: bactopia/GCF_000292685/tools/emmtyper/logs/nf-emmtyper.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/emmtyper/logs/nf-emmtyper.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/emmtyper/logs/nf-emmtyper.sh
      contains: ['emmtyper', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/emmtyper/logs/nf-emmtyper.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/emmtyper/logs/versions.yml
      md5sum: 0bbf84bc5cfd09b4f12594ce3784d08b
    - path: bactopia/GCF_000292685/tools/genotyphi/GCF_000292685.csv
      contains: ["susceptibility", "typhi", "variants"]
    - path: bactopia/GCF_000292685/tools/genotyphi/GCF_000292685.json
      contains: ["susceptibility", "typhi", "predictor"]
    - path: bactopia/GCF_000292685/tools/genotyphi/GCF_000292685_predictResults.tsv
      contains: ['genome', 'GCF_000292685', 'typhi']
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/genotyphi/nf-genotyphi.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/genotyphi/nf-genotyphi.err
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/genotyphi/nf-genotyphi.log
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/genotyphi/nf-genotyphi.out
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/genotyphi/nf-genotyphi.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/genotyphi/nf-genotyphi.sh
      contains: ['parse', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/genotyphi/nf-genotyphi.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/genotyphi/versions.yml
      md5sum: 38b07a9cc1c7298477a20855bb811407
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/mykrobe/nf-genotyphi.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/mykrobe/nf-genotyphi.err
      contains: ['mykrobe', 'typhi', 'finished']
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/mykrobe/nf-genotyphi.log
      contains: ['mykrobe', 'typhi', 'finished']
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/mykrobe/nf-genotyphi.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/mykrobe/nf-genotyphi.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/mykrobe/nf-genotyphi.sh
      contains: ['mykrobe', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/mykrobe/nf-genotyphi.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/genotyphi/logs/mykrobe/versions.yml
      md5sum: 9cdfd2c4d37bb5cea0e119855ebcdbbb
    - path: bactopia/GCF_000292685/tools/hicap/GCF_000292685.tsv
      md5sum: d0e5562f06fa63e264e3c1d2ffee580b
    - path: bactopia/GCF_000292685/tools/hicap/logs/nf-hicap.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/hicap/logs/nf-hicap.err
      contains: ['dependencies', 'ORFs', 'No hits']
    - path: bactopia/GCF_000292685/tools/hicap/logs/nf-hicap.log
      contains: ['dependencies', 'ORFs', 'No hits']
    - path: bactopia/GCF_000292685/tools/hicap/logs/nf-hicap.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/hicap/logs/nf-hicap.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/hicap/logs/nf-hicap.sh
      contains: ['hicap', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/hicap/logs/nf-hicap.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/hicap/logs/versions.yml
      md5sum: 0b1257a5aa492ea30bc3201fc2afcdb7
    - path: bactopia/GCF_000292685/tools/hpsuissero/GCF_000292685_serotyping_res.tsv
      md5sum: 9a26304dc4e57bd347045deecfaac0a6
    - path: bactopia/GCF_000292685/tools/hpsuissero/logs/nf-hpsuissero.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/hpsuissero/logs/nf-hpsuissero.err
    - path: bactopia/GCF_000292685/tools/hpsuissero/logs/nf-hpsuissero.log
      contains: ["Finished"]
    - path: bactopia/GCF_000292685/tools/hpsuissero/logs/nf-hpsuissero.out
      contains: ["Finished"]
    - path: bactopia/GCF_000292685/tools/hpsuissero/logs/nf-hpsuissero.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/hpsuissero/logs/nf-hpsuissero.sh
      contains: ["HpsuisSero", "END_VERSIONS"]
    - path: bactopia/GCF_000292685/tools/hpsuissero/logs/nf-hpsuissero.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/hpsuissero/logs/versions.yml
      md5sum: eaec88a7d7a11910c868a48b8a8cbc5e
    - path: bactopia/GCF_000292685/tools/kleborate/GCF_000292685.results.txt
      md5sum: 69fffd648e56dd1ffaa57bdca43ca560
    - path: bactopia/GCF_000292685/tools/kleborate/logs/nf-kleborate.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/kleborate/logs/nf-kleborate.err
    - path: bactopia/GCF_000292685/tools/kleborate/logs/nf-kleborate.log
      contains: ['strain', 'GCF_000292685']
    - path: bactopia/GCF_000292685/tools/kleborate/logs/nf-kleborate.out
      contains: ['strain', 'GCF_000292685']
    - path: bactopia/GCF_000292685/tools/kleborate/logs/nf-kleborate.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/kleborate/logs/nf-kleborate.sh
      contains: ['kleborate', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/kleborate/logs/nf-kleborate.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/kleborate/logs/versions.yml
      md5sum: 08f5908250d8ea7c55220d528ebfb305
    - path: bactopia/GCF_000292685/tools/legsta/GCF_000292685.tsv
      md5sum: ef72b8e2104dfcce33ee836450670200
    - path: bactopia/GCF_000292685/tools/legsta/logs/nf-legsta.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/legsta/logs/nf-legsta.err
    - path: bactopia/GCF_000292685/tools/legsta/logs/nf-legsta.log
    - path: bactopia/GCF_000292685/tools/legsta/logs/nf-legsta.out
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