- name: busco-test
  command: bash -c 'nextflow run ./subworkflows/local/busco/test.nf -entry test_busco --wf busco -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - busco
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/busco/merged-results/busco.tsv
      md5sum: 15267d2162b35514e27bfca0a32b8e5c
    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.begin
    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/versions.yml
      md5sum: b45e81d6e1c8a0b37a7b3ea491992002
    - path: bactopia/bactopia-runs/busco/nf-reports/busco-dag.dot
      contains: ['buscodag', 'BUSCO', 'versions']
    - path: bactopia/bactopia-runs/busco/nf-reports/busco-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/busco/nf-reports/busco-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/busco/nf-reports/busco-trace.txt
      contains: ['task_id']
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/GCF_000292685-summary.txt
      md5sum: 15267d2162b35514e27bfca0a32b8e5c
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/bbtools_err.log
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/bbtools_out.log
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/busco.log
      contains: ['BuscoConfig', 'busco', 'mode']
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/hmmsearch_err.log
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/hmmsearch_out.log
      contains: ["hmmsearch", "summary", "CPU"]
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/nf-busco.begin
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/nf-busco.err
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/nf-busco.log
      contains: ["Start", "Fragmented", "done"]
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/nf-busco.out
      contains: ["Start", "Fragmented", "done"]
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/nf-busco.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/nf-busco.sh
      contains: ['busco', 'END_VERSIONS']
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/nf-busco.trace
      contains: ['nextflow.trace']
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/prodigal_err.log
      md5sum: c1fdc6977332f53dfe7f632733bb4585
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/prodigal_mode_single_code_11_err.log
      md5sum: c1fdc6977332f53dfe7f632733bb4585
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/prodigal_mode_single_code_11_out.log
      md5sum: 50752acb1c5a20be886bfdfc06635bcb
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/prodigal_out.log
      md5sum: 50752acb1c5a20be886bfdfc06635bcb
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/versions.yml
      md5sum: fdd6b94718c21dd4c370acf841aafc92
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/prodigal_output/.checkpoint
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/prodigal_output/predicted_genes/predicted.faa
      md5sum: 8166471fc5f08c82fd5643ab42327f9d
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/prodigal_output/predicted_genes/predicted.fna
      md5sum: ddc508a18f60e7f3314534df50cdf8ca
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
      md5sum: 8166471fc5f08c82fd5643ab42327f9d
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
      md5sum: ddc508a18f60e7f3314534df50cdf8ca
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/.bbtools_output/.checkpoint
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1272633at2.faa
      md5sum: bc3d8e3ec26129fb17110134822fc8cd
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1272633at2.fna
      md5sum: c9d955773c7433464d5886d56c4cbf58
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1054741at2.faa
      md5sum: a8f004eb3c63433eafe2e3886e680c85
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1054741at2.fna
      md5sum: bb5835b69e7e09f1661a09b75df4887b
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1132353at2.faa
      md5sum: 85494768d2a27813a97e2e55e3e8424b
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1132353at2.fna
      md5sum: 955560ad0799a224a8e2c0ea033a91a7
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/961486at2.faa
      md5sum: e70105bd9c0a92b6d442d9d48333e22a
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/961486at2.fna
      md5sum: 421d326188a45e6e0101a5448e200ba5
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/full_table.tsv
      md5sum: c9651b88b10871abc260ee655898e828
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/hmmer_output/.checkpoint
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/hmmer_output/1054741at2.out
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/hmmer_output/1132353at2.out
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/hmmer_output/961486at2.out
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/missing_busco_list.tsv
      md5sum: 9939309df2da5419de88c32d1435c779
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/short_summary.json
      contains: ["one_line_summary", "dataset"]
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/short_summary.txt
      contains: ["BUSCO", "Dependencies", "Total"]
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/short_summary.specific.bacteria_odb10.GCF_000292685.fna.json
      contains: ["one_line_summary", "dataset"]
    - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/short_summary.specific.bacteria_odb10.GCF_000292685.fna.txt
      contains: ["BUSCO", "Dependencies", "Total"]
