- name: checkm-test
  command: bash -c 'nextflow run ./subworkflows/local/checkm/test.nf -entry test_checkm --wf checkm -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - checkm
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/checkm/merged-results/checkm.tsv
      md5sum: 3a76623c675e0e6e12a987da198c6f5d
    - path: bactopia/bactopia-runs/checkm/merged-results/logs/checkm-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/checkm/merged-results/logs/checkm-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/checkm/merged-results/logs/checkm-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/checkm/merged-results/logs/checkm-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/checkm/merged-results/logs/checkm-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/checkm/merged-results/logs/checkm-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/checkm/merged-results/logs/checkm-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/checkm/merged-results/logs/checkm-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/checkm/nf-reports/checkm-dag.dot
      contains: ['checkmdag', 'checkm', 'CHECKM']
    - path: bactopia/bactopia-runs/checkm/nf-reports/checkm-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/checkm/nf-reports/checkm-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/checkm/nf-reports/checkm-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000292685/tools/checkm/GCF_000292685-genes.aln
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/checkm/GCF_000292685-results.txt
      md5sum: 3a76623c675e0e6e12a987da198c6f5d
    - path: bactopia/GCF_000292685/tools/checkm/bins/GCF_000292685/genes.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/bins/GCF_000292685/genes.gff
    - path: bactopia/GCF_000292685/tools/checkm/bins/GCF_000292685/hmmer.analyze.txt.gz
    - path: bactopia/GCF_000292685/tools/checkm/bins/GCF_000292685/hmmer.tree.txt
      contains: ["target", "ID", "Ribosomal"]
    - path: bactopia/GCF_000292685/tools/checkm/lineage.ms
      contains: ['Lineage Marker File']
    - path: bactopia/GCF_000292685/tools/checkm/logs/checkm.log
      contains: ['CheckM', 'Parsing', 'written']
    - path: bactopia/GCF_000292685/tools/checkm/logs/nf-checkm.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/GCF_000292685/tools/checkm/logs/nf-checkm.err
      contains: ['Finished', 'parsing', 'hits']
    - path: bactopia/GCF_000292685/tools/checkm/logs/nf-checkm.log
      contains: ['Finished', 'Parsing', 'hits', 'CheckM']
    - path: bactopia/GCF_000292685/tools/checkm/logs/nf-checkm.out
      contains: ['CheckM', 'Parsing', 'written']
    - path: bactopia/GCF_000292685/tools/checkm/logs/nf-checkm.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/checkm/logs/nf-checkm.sh
      contains: ['checkm', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/checkm/logs/nf-checkm.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/checkm/logs/versions.yml
      md5sum: f35b50ae944a85f80dd1b3ad0ff479c4
    - path: bactopia/GCF_000292685/tools/checkm/storage/bin_stats.analyze.tsv
    - path: bactopia/GCF_000292685/tools/checkm/storage/bin_stats.tree.tsv
    - path: bactopia/GCF_000292685/tools/checkm/storage/bin_stats_ext.tsv
      contains: ['marker lineage']
    - path: bactopia/GCF_000292685/tools/checkm/storage/checkm_hmm_info.pkl.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/marker_gene_stats.tsv
      contains: ['GCF_000292685']
    - path: bactopia/GCF_000292685/tools/checkm/storage/phylo_hmm_info.pkl.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00164.20.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00177.16.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00181.18.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00189.15.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00203.16.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00237.14.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00238.14.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00252.13.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00276.15.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00281.14.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00297.17.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00298.14.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00312.17.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00318.15.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00333.15.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00366.15.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00380.14.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00410.14.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00411.14.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00466.15.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00562.23.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00572.13.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00573.17.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00623.15.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00673.16.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00687.16.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00831.18.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF00861.17.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF03719.10.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF03946.9.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF03947.13.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF04560.15.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF04561.9.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF04563.10.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF04565.11.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF04997.7.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF05000.12.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/PF11987.3.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/TIGR00422.masked.faa.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/concatenated.fasta.gz
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/concatenated.pplacer.json
      contains: ['metadata', 'pplacer']
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/concatenated.tre
      md5sum: 478880ccdff6d05c9e7f130773f717c3
    - path: bactopia/GCF_000292685/tools/checkm/storage/tree/pplacer.out
      md5sum: 461c332efb29e100721ceaffb65bd725
