- name: quast-test
  command: bash -c 'nextflow run ./subworkflows/local/quast/test.nf -entry test_quast --wf quast -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - quast
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/quast/merged-results/logs/quast-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/quast/merged-results/logs/quast-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/quast/merged-results/logs/quast-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/quast/merged-results/logs/quast-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/quast/merged-results/logs/quast-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/quast/merged-results/logs/quast-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/quast/merged-results/logs/quast-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/quast/merged-results/logs/quast-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/quast/merged-results/quast.tsv
      contains: ["Assembly", "contigs", "predicted", "NG90"]
    - path: bactopia/bactopia-runs/quast/nf-reports/quast-dag.dot
      contains: ['quastdag', 'QUAST', 'versions']
    - path: bactopia/bactopia-runs/quast/nf-reports/quast-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/quast/nf-reports/quast-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/quast/nf-reports/quast-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000292685/tools/quast/GCF_000292685.tsv
      contains: ["Assembly", "contigs", "predicted", "NG90"]
    - path: bactopia/GCF_000292685/tools/quast/basic_stats/GCF_000292685_GC_content_plot.pdf
    - path: bactopia/GCF_000292685/tools/quast/basic_stats/GC_content_plot.pdf
    - path: bactopia/GCF_000292685/tools/quast/basic_stats/NGx_plot.pdf
    - path: bactopia/GCF_000292685/tools/quast/basic_stats/Nx_plot.pdf
    - path: bactopia/GCF_000292685/tools/quast/basic_stats/cumulative_plot.pdf
    - path: bactopia/GCF_000292685/tools/quast/icarus.html
    - path: bactopia/GCF_000292685/tools/quast/icarus_viewers/contig_size_viewer.html
    - path: bactopia/GCF_000292685/tools/quast/logs/nf-quast.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/quast/logs/nf-quast.err
    - path: bactopia/GCF_000292685/tools/quast/logs/nf-quast.log
      contains: ["Creating", "Contig", "versions", "QUAST"]
    - path: bactopia/GCF_000292685/tools/quast/logs/nf-quast.out
      contains: ["Creating", "Contig", "versions", "QUAST"]
    - path: bactopia/GCF_000292685/tools/quast/logs/nf-quast.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/quast/logs/nf-quast.sh
      contains: ['quast', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/quast/logs/nf-quast.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/quast/logs/quast.log
      contains: ['Version', 'QUAST']
    - path: bactopia/GCF_000292685/tools/quast/logs/versions.yml
      md5sum: 7dae1e03b0d1199851a1c393bc72c039
    - path: bactopia/GCF_000292685/tools/quast/predicted_genes/GCF_000292685_glimmer.stderr
      md5sum: 390dc7df727903e33d8127f8f12d9cf5
    - path: bactopia/GCF_000292685/tools/quast/predicted_genes/GCF_000292685_glimmer_genes.gff
      contains: ["version", "NC_018507", "CDS", "exon"]
    - path: bactopia/GCF_000292685/tools/quast/report.html
      contains: ['QUAST']
    - path: bactopia/GCF_000292685/tools/quast/report.pdf
    - path: bactopia/GCF_000292685/tools/quast/report.tex
      contains: ["Assembly", "contigs", "predicted", "NG90"]
    - path: bactopia/GCF_000292685/tools/quast/report.tsv
      contains: ["Assembly", "contigs", "predicted", "NG90"]
    - path: bactopia/GCF_000292685/tools/quast/report.txt
      contains: ["Assembly", "contigs", "predicted", "NG90"]
    - path: bactopia/GCF_000292685/tools/quast/transposed_report.tex
      contains: ["Assembly", "contigs", "predicted", "NG90"]
    - path: bactopia/GCF_000292685/tools/quast/transposed_report.txt
      contains: ["Assembly", "contigs", "predicted", "NG90"]
