- name: eggnog-test
  command: bash -c 'nextflow run ./subworkflows/local/eggnog/test.nf -entry test_eggnog --wf eggnog -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - eggnog
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/eggnog/nf-reports/eggnog-dag.dot
      contains: ['eggnogdag', 'EGGNOG', 'versions']
    - path: bactopia/bactopia-runs/eggnog/nf-reports/eggnog-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/eggnog/nf-reports/eggnog-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/eggnog/nf-reports/eggnog-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000292685/tools/eggnog/GCF_000292685.emapper.annotations
      contains: ['emapper', 'Gammaproteobacteria', 'scanned']
    - path: bactopia/GCF_000292685/tools/eggnog/GCF_000292685.emapper.hits
      contains: ['WP_014894920']
    - path: bactopia/GCF_000292685/tools/eggnog/GCF_000292685.emapper.seed_orthologs
      contains: ['emapper', 'diamond', 'scanned']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.err
      contains: ['Functional']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.log
      contains: ['Functional', 'eggNOG', 'FINISHED']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.out
      contains: ['Functional', 'eggNOG', 'FINISHED']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.sh
      contains: ['eggnog', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/versions.yml
      md5sum: 14296ed2973e741f22b0c5f87a137925

- name: eggnog-test-tarball
  command: bash -c 'nextflow run ./subworkflows/local/eggnog/test.nf -entry test_eggnog_tarball --wf eggnog -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - eggnog
    - eggnog-tarball
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/eggnog/nf-reports/eggnog-dag.dot
      contains: ['eggnogdag', 'EGGNOG', 'versions']
    - path: bactopia/bactopia-runs/eggnog/nf-reports/eggnog-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/eggnog/nf-reports/eggnog-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/eggnog/nf-reports/eggnog-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000292685/tools/eggnog/GCF_000292685.emapper.annotations
      contains: ['emapper', 'Gammaproteobacteria', 'scanned']
    - path: bactopia/GCF_000292685/tools/eggnog/GCF_000292685.emapper.hits
      contains: ['WP_014894920']
    - path: bactopia/GCF_000292685/tools/eggnog/GCF_000292685.emapper.seed_orthologs
      contains: ['emapper', 'diamond', 'scanned']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.err
      contains: ['Functional']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.log
      contains: ['Functional', 'eggNOG', 'FINISHED']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.out
      contains: ['Functional', 'eggNOG', 'FINISHED']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.sh
      contains: ['eggnog', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/nf-eggnog.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/eggnog/logs/versions.yml
      md5sum: 246a2309cb9bdfab73cc8193320eeb11
