- name: blastn-test
  command: bash -c 'nextflow run ./subworkflows/local/blastn/test.nf -entry test_blastn --wf blastn -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - blastn
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/blastn/merged-results/blastn.tsv
      md5sum: 3a6bc3a4b38b150e79573aa8838af21d
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/blastn/nf-reports/blastn-dag.dot
      contains: ['blastndag', 'BLASTN', 'versions']
    - path: bactopia/bactopia-runs/blastn/nf-reports/blastn-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/blastn/nf-reports/blastn-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/blastn/nf-reports/blastn-trace.txt
      contains: ['task_id']
    - path: bactopia/SRX1390622/tools/blastn/SRX1390622.blastn.tsv
      md5sum: 3a6bc3a4b38b150e79573aa8838af21d
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.err
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.log
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.out
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.sh
      contains: ['blastn', 'END_VERSIONS']
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRX1390622/tools/blastn/logs/versions.yml
      md5sum: 05f4d83f9689ca445c89d2c14286042e

- name: blastn-test_gz
  command: bash -c 'nextflow run ./subworkflows/local/blastn/test.nf -entry test_blastn_gz --wf blastn -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - blastn
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/blastn/merged-results/blastn.tsv
      md5sum: 3a6bc3a4b38b150e79573aa8838af21d
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/blastn/nf-reports/blastn-dag.dot
      contains: ['blastndag', 'BLASTN', 'versions']
    - path: bactopia/bactopia-runs/blastn/nf-reports/blastn-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/blastn/nf-reports/blastn-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/blastn/nf-reports/blastn-trace.txt
      contains: ['task_id']
    - path: bactopia/SRX1390622/tools/blastn/SRX1390622.blastn.tsv
      md5sum: 3a6bc3a4b38b150e79573aa8838af21d
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.err
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.log
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.out
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.sh
      contains: ['blastn', 'END_VERSIONS']
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRX1390622/tools/blastn/logs/versions.yml
      md5sum: 265c014c7328186a307cb9430da090af

- name: blastn-test_use_genes
  command: bash -c 'nextflow run ./subworkflows/local/blastn/test.nf -entry test_blastn_use_genes --wf blastn -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - blastn
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/blastn/merged-results/blastn.tsv
      md5sum: e701af518b39079126c32b6636e84e01
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/blastn/merged-results/logs/blastn-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/blastn/nf-reports/blastn-dag.dot
      contains: ['blastndag', 'BLASTN', 'versions']
    - path: bactopia/bactopia-runs/blastn/nf-reports/blastn-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/blastn/nf-reports/blastn-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/blastn/nf-reports/blastn-trace.txt
      contains: ['task_id']
    - path: bactopia/SRX1390622/tools/blastn/SRX1390622.blastn.tsv
      md5sum: e701af518b39079126c32b6636e84e01
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.err
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.log
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.out
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.sh
      contains: ['blastn', 'END_VERSIONS']
    - path: bactopia/SRX1390622/tools/blastn/logs/nf-blastn.trace
      contains: ['nextflow.trace']
    - path: bactopia/SRX1390622/tools/blastn/logs/versions.yml
      md5sum: 0ff2ad9ce7ba1cc1fad83f8d59143d95
