- name: shigatyper-test_pe
  command: bash -c 'nextflow run ./subworkflows/local/shigatyper/test.nf -entry test_shigatyper_pe --wf shigatyper -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - shigatyper
    - shigatyper_pe
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/shigatyper/merged-results/shigatyper.tsv
      md5sum: 84bc68331bf503ea23da27207e418383
    - path: bactopia/bactopia-runs/shigatyper/nf-reports/shigatyper-dag.dot
      contains: ['shigatyperdag', 'SHIGATYPER', 'versions']
    - path: bactopia/bactopia-runs/shigatyper/nf-reports/shigatyper-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/shigatyper/nf-reports/shigatyper-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/shigatyper/nf-reports/shigatyper-trace.txt
      contains: ['task_id']
    - path: bactopia/ERR6005894/tools/shigatyper/ERR6005894-hits.tsv
      md5sum: 86324f1cdc686eb68b85bd27776a8dc7
    - path: bactopia/ERR6005894/tools/shigatyper/ERR6005894.tsv
      md5sum: 84bc68331bf503ea23da27207e418383
    - path: bactopia/ERR6005894/tools/shigatyper/logs/nf-shigatyper.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/ERR6005894/tools/shigatyper/logs/nf-shigatyper.err
      contains: ["ShigaTyper", "ShigellaRef5", "dysenteriae"]
    - path: bactopia/ERR6005894/tools/shigatyper/logs/nf-shigatyper.log
      contains: ["ShigaTyper", "ShigellaRef5", "dysenteriae"]
    - path: bactopia/ERR6005894/tools/shigatyper/logs/nf-shigatyper.out
    - path: bactopia/ERR6005894/tools/shigatyper/logs/nf-shigatyper.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/ERR6005894/tools/shigatyper/logs/nf-shigatyper.sh
      contains: ['shigatyper', 'END_VERSIONS']
    - path: bactopia/ERR6005894/tools/shigatyper/logs/nf-shigatyper.trace
      contains: ['nextflow.trace']
    - path: bactopia/ERR6005894/tools/shigatyper/logs/versions.yml
      md5sum: c0e1211b427491e0c4e8c060de2bc31c

- name: shigatyper-test_se
  command: bash -c 'nextflow run ./subworkflows/local/shigatyper/test.nf -entry test_shigatyper_se --wf shigatyper -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - shigatyper
    - shigatyper_se
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/shigatyper/merged-results/shigatyper.tsv
      md5sum: 56b194ae479ed5118a2f1560d0365386
    - path: bactopia/bactopia-runs/shigatyper/nf-reports/shigatyper-dag.dot
      contains: ['shigatyperdag', 'SHIGATYPER', 'versions']
    - path: bactopia/bactopia-runs/shigatyper/nf-reports/shigatyper-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/shigatyper/nf-reports/shigatyper-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/shigatyper/nf-reports/shigatyper-trace.txt
      contains: ['task_id']
    - path: bactopia/ERR6005894SE/tools/shigatyper/ERR6005894SE-hits.tsv
      md5sum: 3a2660886597dbb4e9d6f3990a36785f
    - path: bactopia/ERR6005894SE/tools/shigatyper/ERR6005894SE.tsv
      md5sum: 56b194ae479ed5118a2f1560d0365386
    - path: bactopia/ERR6005894SE/tools/shigatyper/logs/nf-shigatyper.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/ERR6005894SE/tools/shigatyper/logs/nf-shigatyper.err
      contains: ["ShigaTyper", "ShigellaRef5", "dysenteriae"]
    - path: bactopia/ERR6005894SE/tools/shigatyper/logs/nf-shigatyper.log
      contains: ["ShigaTyper", "ShigellaRef5", "dysenteriae"]
    - path: bactopia/ERR6005894SE/tools/shigatyper/logs/nf-shigatyper.out
    - path: bactopia/ERR6005894SE/tools/shigatyper/logs/nf-shigatyper.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/ERR6005894SE/tools/shigatyper/logs/nf-shigatyper.sh
      contains: ['shigatyper', 'END_VERSIONS']
    - path: bactopia/ERR6005894SE/tools/shigatyper/logs/nf-shigatyper.trace
      contains: ['nextflow.trace']
    - path: bactopia/ERR6005894SE/tools/shigatyper/logs/versions.yml
      md5sum: 0939923702e0d3d3693bbb49e3bb1d48

- name: shigatyper-test_ont
  command: bash -c 'nextflow run ./subworkflows/local/shigatyper/test.nf -entry test_shigatyper_ont --wf shigatyper -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - shigatyper
    - shigatyper_ont
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/shigatyper/merged-results/logs/shigatyper-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/shigatyper/merged-results/shigatyper.tsv
      md5sum: 8ab32470875fe923b8d338da4ca35d1c
    - path: bactopia/bactopia-runs/shigatyper/nf-reports/shigatyper-dag.dot
      contains: ['shigatyperdag', 'SHIGATYPER', 'versions']
    - path: bactopia/bactopia-runs/shigatyper/nf-reports/shigatyper-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/shigatyper/nf-reports/shigatyper-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/shigatyper/nf-reports/shigatyper-trace.txt
      contains: ['task_id']
    - path: bactopia/SRR13039589/tools/shigatyper/SRR13039589-hits.tsv
      md5sum: 7bdab5d495d8424b2df3005773ef1364
    - path: bactopia/SRR13039589/tools/shigatyper/SRR13039589.tsv
      md5sum: 8ab32470875fe923b8d338da4ca35d1c
    - path: bactopia/SRR13039589/tools/shigatyper/logs/nf-shigatyper.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR13039589/tools/shigatyper/logs/nf-shigatyper.err
      contains: ["ShigaTyper", "ShigellaRef5", "EIEC"]
    - path: bactopia/SRR13039589/tools/shigatyper/logs/nf-shigatyper.log
      contains: ["ShigaTyper", "ShigellaRef5", "EIEC"]
    - path: bactopia/SRR13039589/tools/shigatyper/logs/nf-shigatyper.out
    - path: bactopia/SRR13039589/tools/shigatyper/logs/nf-shigatyper.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRR13039589/tools/shigatyper/logs/nf-shigatyper.sh
      contains: ['shigatyper', 'END_VERSIONS']
    - path: bactopia/SRR13039589/tools/shigatyper/logs/nf-shigatyper.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRR13039589/tools/shigatyper/logs/versions.yml
      md5sum: f7a3bb24758471c13fcf8c2dd3cf16ba
