- name: midas-test
  command: bash -c 'nextflow run ./subworkflows/local/midas/test.nf -entry test_midas --wf midas -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - midas
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/midas/merged-results/midas.tsv
      contains: ['SRR2838702', 'primary', 'secondary']
    - path: bactopia/bactopia-runs/midas/nf-reports/midas-dag.dot
      contains: ['midasdag', 'MIDAS_SPECIES', 'versions']
    - path: bactopia/bactopia-runs/midas/nf-reports/midas-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/midas/nf-reports/midas-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/midas/nf-reports/midas-trace.txt
      contains: ['task_id']
    - path: bactopia/SRR2838702/tools/midas/SRR2838702.midas.abundances.txt
      contains: ['species_id', 'Bacillus']
    - path: bactopia/SRR2838702/tools/midas/SRR2838702.midas.adjusted.abundances.txt
      contains: ['species_id', 'Bacillus']
    - path: bactopia/SRR2838702/tools/midas/SRR2838702.midas.tsv
      contains: ['SRR2838702', 'primary', 'secondary']
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.err
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.log
      contains: ['MIDAS', 'Command', 'Classifying']
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.out
      contains: ['MIDAS', 'Command', 'Classifying']
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.sh
      contains: ['run_midas', 'END_VERSIONS']
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRR2838702/tools/midas/logs/versions.yml
      md5sum: 4e71a163042a3c1bcdb42357031240ce

- name: midas-test-tarball
  command: bash -c 'nextflow run ./subworkflows/local/midas/test.nf -entry test_midas_tarball --wf midas -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - midas
    - midas-tarball
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/midas/merged-results/logs/midas-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/midas/merged-results/midas.tsv
      contains: ['SRR2838702', 'primary', 'secondary']
    - path: bactopia/bactopia-runs/midas/nf-reports/midas-dag.dot
      contains: ['midasdag', 'MIDAS_SPECIES', 'versions']
    - path: bactopia/bactopia-runs/midas/nf-reports/midas-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/midas/nf-reports/midas-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/midas/nf-reports/midas-trace.txt
      contains: ['task_id']
    - path: bactopia/SRR2838702/tools/midas/SRR2838702.midas.abundances.txt
      contains: ['species_id', 'Bacillus']
    - path: bactopia/SRR2838702/tools/midas/SRR2838702.midas.adjusted.abundances.txt
      contains: ['species_id', 'Bacillus']
    - path: bactopia/SRR2838702/tools/midas/SRR2838702.midas.tsv
      contains: ['SRR2838702', 'primary', 'secondary']
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.err
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.log
      contains: ['MIDAS', 'Command', 'Classifying']
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.out
      contains: ['MIDAS', 'Command', 'Classifying']
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.sh
      contains: ['run_midas', 'END_VERSIONS']
    - path: bactopia/SRR2838702/tools/midas/logs/nf-midas.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRR2838702/tools/midas/logs/versions.yml
      md5sum: 492059fdd4d2e2c34e8ffb0d62a33cc5
