- name: busco test_busco_genome_single_fasta
  command: nextflow run tests/modules/busco -entry test_busco_genome_single_fasta -c tests/config/nextflow.config
  tags:
    - busco
  files:
    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
      contains:
        - "one_line_summary"
        - "input_file"
        - "mode"
        - "dataset"
    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
      contains:
        - "BUSCO version"
        - "The lineage dataset is"
        - "BUSCO was run in mode"
        - "Complete BUSCOs"
        - "Missing BUSCOs"
        - "Dependencies and versions"
    - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.json
      contains:
        - "one_line_summary"
        - "input_file"
        - "mode"
        - "dataset"
    - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
      contains:
        - "BUSCO version"
        - "The lineage dataset is"
        - "BUSCO was run in mode"
        - "Complete BUSCOs"
        - "Missing BUSCOs"
        - "Dependencies and versions"
    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
      md5sum: e50690742e9ae6abdd2bf99334ff9e12
    - path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt
      md5sum: 4c1b2c4317c88398eddc30877ed740d9
    - path: output/busco/versions.yml
      md5sum: 8aa830f71587d859df35c6cfab59f35d

- name: busco test_busco_genome_multi_fasta
  command: nextflow run tests/modules/busco -entry test_busco_genome_multi_fasta -c tests/config/nextflow.config
  tags:
    - busco
  files:
    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.json
      contains:
        - "one_line_summary"
        - "input_file"
        - "mode"
        - "dataset"
    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.txt
      contains:
        - "BUSCO version"
        - "The lineage dataset is"
        - "BUSCO was run in mode"
        - "Complete BUSCOs"
        - "Missing BUSCOs"
        - "Dependencies and versions"
    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
      contains:
        - "one_line_summary"
        - "input_file"
        - "mode"
        - "dataset"
    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
      contains:
        - "BUSCO version"
        - "The lineage dataset is"
        - "BUSCO was run in mode"
        - "Complete BUSCOs"
        - "Missing BUSCOs"
        - "Dependencies and versions"
    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
      contains:
        - "Input_file"
        - "Dataset"
        - "Complete"
        - "Single"
        - "Duplicated"
        - "Fragmented"
        - "Missing"
        - "n_markers"
        - "genome.fasta"
        - "genome.fna"
        - "bacteria_odb10"
    - path: output/busco/versions.yml
      md5sum: 9a959eb0a1f765777dff1ea2f5c139c0

- name: busco test_busco_eukaryote_metaeuk
  command: nextflow run tests/modules/busco -entry test_busco_eukaryote_metaeuk -c tests/config/nextflow.config
  tags:
    - busco
  files:
    - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.json
      contains:
        - "one_line_summary"
        - "input_file"
        - "mode"
        - "dataset"
    - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.txt
      contains:
        - "BUSCO version"
        - "The lineage dataset is"
        - "BUSCO was run in mode"
        - "Complete BUSCOs"
        - "Missing BUSCOs"
        - "Dependencies and versions"
    - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
      md5sum: a70806f99ba5706d7353d3353b3f1d2b
    - path: output/busco/versions.yml
      md5sum: 34a808c257e6db1b0456f3b4372bc477

- name: busco test_busco_eukaryote_augustus
  command: nextflow run tests/modules/busco -entry test_busco_eukaryote_augustus -c tests/config/nextflow.config
  tags:
    - busco
  files:
    - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
      md5sum: 660393dd43cd6a093b952d4b8ad41e40
    - path: output/busco/versions.yml
      md5sum: 2caac915461410b16a1524ac064cd0df

- name: busco test_busco_protein
  command: nextflow run tests/modules/busco -entry test_busco_protein -c tests/config/nextflow.config
  tags:
    - busco
  files:
    - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.json
      contains:
        - "one_line_summary"
        - "input_file"
        - "mode"
        - "dataset"
    - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.txt
      contains:
        - "BUSCO version"
        - "The lineage dataset is"
        - "BUSCO was run in mode"
        - "Complete BUSCOs"
        - "Missing BUSCOs"
        - "Dependencies and versions"
    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
      md5sum: fd3b4e30ce74d1fcb95d6286d6e2049f
    - path: output/busco/versions.yml
      md5sum: d7392261a57960a7e6aea609dce824f5

- name: busco test_busco_transcriptome
  command: nextflow run tests/modules/busco -entry test_busco_transcriptome -c tests/config/nextflow.config
  tags:
    - busco
  files:
    - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
      contains:
        - "one_line_summary"
        - "input_file"
        - "mode"
        - "dataset"
    - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
      contains:
        - "BUSCO version"
        - "The lineage dataset is"
        - "BUSCO was run in mode"
        - "Complete BUSCOs"
        - "Missing BUSCOs"
        - "Dependencies and versions"
    - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
      md5sum: 9a176cafe66ac0adca89dc34ad2be13f
    - path: output/busco/versions.yml
      md5sum: 30eacbc7df70f6b1e72e0a7b6d02a7e1