- name: sketcher-pe
  command: bash -c 'nextflow run ./subworkflows/local/sketcher/test.nf -entry test_sketcher_pe -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - bactopia
    - sketcher
    - sketcher_pe
  files:
    - path: bactopia/bactopia-runs/bactopia/nf-reports/bactopia-dag.dot
      contains: ['bactopiadag', 'SKETCHER', 'versions']
    - path: bactopia/bactopia-runs/bactopia/nf-reports/bactopia-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/bactopia/nf-reports/bactopia-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/bactopia/nf-reports/bactopia-trace.txt
      contains: ['task_id']
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.err
      contains: ['Estimated', 'coverage', 'sourmash', 'saved']
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.log
      contains: ['Estimated', 'coverage', 'sourmash', 'saved']
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.out
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.sh
      contains: ['mash', 'sourmash', 'END_VERSIONS']
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.trace
      contains: ['nextflow.trace']
    - path: bactopia/output/main/sketcher/logs/versions.yml
      md5sum: 34c3efbea4984d9b4c2626797915d5ea
    - path: bactopia/output/main/sketcher/output-k21.msh
    - path: bactopia/output/main/sketcher/output-k31.msh
    - path: bactopia/output/main/sketcher/output-mash-refseq88-k21.txt
      md5sum: f095a76d9e71aa814be756ef413b626c
    - path: bactopia/output/main/sketcher/output-sourmash-gtdb-rs207-k31.txt
      md5sum: 733b0d2c06b8f9c1a70f2da3ca8a5b96
    - path: bactopia/output/main/sketcher/output.sig

- name: sketcher-se
  command: bash -c 'nextflow run ./subworkflows/local/sketcher/test.nf -entry test_sketcher_se -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - bactopia
    - sketcher
    - sketcher_se
  files:
    - path: bactopia/bactopia-runs/bactopia/nf-reports/bactopia-dag.dot
      contains: ['bactopiadag', 'SKETCHER', 'versions']
    - path: bactopia/bactopia-runs/bactopia/nf-reports/bactopia-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/bactopia/nf-reports/bactopia-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/bactopia/nf-reports/bactopia-trace.txt
      contains: ['task_id']
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.err
      contains: ['Estimated', 'coverage', 'sourmash', 'saved']
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.log
      contains: ['Estimated', 'coverage', 'sourmash', 'saved']
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.out
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.sh
      contains: ['mash', 'sourmash', 'END_VERSIONS']
    - path: bactopia/output/main/sketcher/logs/nf-sketcher.trace
      contains: ['nextflow.trace']
    - path: bactopia/output/main/sketcher/logs/versions.yml
      md5sum: c21c9e1e4e3f41a36a5e0116aef269b7
    - path: bactopia/output/main/sketcher/output-k21.msh
    - path: bactopia/output/main/sketcher/output-k31.msh
    - path: bactopia/output/main/sketcher/output-mash-refseq88-k21.txt
      md5sum: 063e00f7f761e2087c4ba02a45e9bafa
    - path: bactopia/output/main/sketcher/output-sourmash-gtdb-rs207-k31.txt
      md5sum: 733b0d2c06b8f9c1a70f2da3ca8a5b96
    - path: bactopia/output/main/sketcher/output.sig
