- name: busco test_busco_genome_single_fasta
  command: nextflow run ./tests/modules/busco -entry test_busco_genome_single_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
  tags:
    - busco
  files:
    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
      contains:
        - "one_line_summary"
        - "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"
        - "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: bc2440f8a68d7fbf931ff911c1c3fdfa
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_err.log
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_out.log
      contains:
        - "IUPAC"
        - "genome scaffold"
        - "Coverage"
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_err.log
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_out.log
      contains:
        - "# hmmsearch :: search profile(s) against a sequence database"
        - "# target sequence database:"
        - "Internal pipeline statistics summary:"
        - "[ok]"
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_err.log
      md5sum: 538510cfc7483498210f01e53fe035ad
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_out.log
      md5sum: 61050b0706addc9498b2088a2d6efa9a
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/.checkpoint
      contains:
        - "Tool: prodigal"
        - "Completed"
        - "jobs"
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
      md5sum: 836e9a80d33d8b89168f07ddc13ee991
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
      md5sum: 836e9a80d33d8b89168f07ddc13ee991
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
      md5sum: 538510cfc7483498210f01e53fe035ad
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
      md5sum: 61050b0706addc9498b2088a2d6efa9a
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/.bbtools_output/.checkpoint
      contains:
        - "Tool: bbtools"
        - "Completed"
        - "jobs"
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/full_table.tsv
      md5sum: 275a7ece09ef61aa59ee7a811289e3d8
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/hmmer_output.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/missing_busco_list.tsv
      md5sum: ab574cde031a3fbff471976ea61e215d
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.json
      contains:
        - "one_line_summary"
        - "mode"
        - "lineage_dataset"
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.txt
      contains:
        - "# BUSCO version is:"
        - "Results:"
        - "busco:"
    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
      contains:
        - "DEBUG:busco.run_BUSCO"
        - "Results from dataset"
        - "how to cite BUSCO"
    - path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt
      md5sum: 5ad8ecfbf4058b059e5edeb9170fc683
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/bbtools_err.log
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/bbtools_out.log
      contains:
        - "IUPAC"
        - "genome scaffold"
        - "Coverage"
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/hmmsearch_err.log
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/hmmsearch_out.log
      contains:
        - "# hmmsearch :: search profile(s) against a sequence database"
        - "# target sequence database:"
        - "Internal pipeline statistics summary:"
        - "[ok]"
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/prodigal_err.log
      md5sum: 538510cfc7483498210f01e53fe035ad
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/prodigal_out.log
      md5sum: 61050b0706addc9498b2088a2d6efa9a
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/.checkpoint
      contains:
        - "Tool: prodigal"
        - "Completed"
        - "jobs"
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
      md5sum: 836e9a80d33d8b89168f07ddc13ee991
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
      md5sum: 836e9a80d33d8b89168f07ddc13ee991
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
      md5sum: 538510cfc7483498210f01e53fe035ad
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
      md5sum: 61050b0706addc9498b2088a2d6efa9a
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/.bbtools_output/.checkpoint
      contains:
        - "Tool: bbtools"
        - "Completed"
        - "jobs"
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/full_table.tsv
      md5sum: 2360bb06f7171dafaa7ebf879789689b
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/hmmer_output.tar.gz
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/missing_busco_list.tsv
      md5sum: e1fb12cf416448d35fbc5c508065963a
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/short_summary.json
      contains:
        - "one_line_summary"
        - "mode"
        - "lineage_dataset"
    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/short_summary.txt
      contains:
        - "# BUSCO version is:"
        - "Results:"
        - "busco:"
    - path: output/busco/test-bacteroidetes_odb10-busco/logs/busco.log
      contains:
        - "DEBUG:busco.run_BUSCO"
        - "Results from dataset"
        - "how to cite BUSCO"

- name: busco test_busco_genome_multi_fasta
  command: nextflow run ./tests/modules/busco -entry test_busco_genome_multi_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
  tags:
    - busco
  files:
    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.json
      contains:
        - "one_line_summary"
        - "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"
        - "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"
        - "genome.fna"
        - "genome.fasta"
        - "bacteria_odb10"
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/bbtools_err.log
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/bbtools_out.log
      contains:
        - "IUPAC"
        - "genome scaffold"
        - "Coverage"
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/hmmsearch_err.log
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/hmmsearch_out.log
      contains:
        - "# hmmsearch :: search profile(s) against a sequence database"
        - "# target sequence database:"
        - "Internal pipeline statistics summary:"
        - "[ok]"
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/prodigal_err.log
      md5sum: c1fdc6977332f53dfe7f632733bb4585
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/logs/prodigal_out.log
      md5sum: 50752acb1c5a20be886bfdfc06635bcb
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/.checkpoint
      contains:
        - "Tool: prodigal"
        - "Completed"
        - "jobs"
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/predicted.faa
      md5sum: 8166471fc5f08c82fd5643ab42327f9d
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/predicted.fna
      md5sum: ddc508a18f60e7f3314534df50cdf8ca
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
      md5sum: 8166471fc5f08c82fd5643ab42327f9d
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
      md5sum: ddc508a18f60e7f3314534df50cdf8ca
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
      md5sum: c1fdc6977332f53dfe7f632733bb4585
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
      md5sum: 50752acb1c5a20be886bfdfc06635bcb
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4.faa
      md5sum: e56fd59c38248dc21ac94355dca98121
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4.fna
      md5sum: b365f84bf99c68357952e0b98ed7ce42
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4_err.log
      md5sum: e5f14d7925ba14a0f9850542f3739894
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4_out.log
      md5sum: d41971bfc1b621d4ffd2633bc47017ea
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/.bbtools_output/.checkpoint
      contains:
        - "Tool: bbtools"
        - "Completed"
        - "jobs"
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/full_table.tsv
      md5sum: f473ded1f1db2463533d51be6ed6fd2d
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/hmmer_output.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/missing_busco_list.tsv
      md5sum: 8e6b6a4ba25caf8e7ad15e8a77064755
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/short_summary.json
      contains:
        - "one_line_summary"
        - "mode"
        - "dataset"
    - path: output/busco/test-bacteria_odb10-busco/genome.fasta/run_bacteria_odb10/short_summary.txt
      contains:
        - "# BUSCO version is:"
        - "Results:"
        - "busco:"
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_err.log
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_out.log
      contains:
        - "IUPAC"
        - "genome scaffold"
        - "Coverage"
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_err.log
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/hmmsearch_out.log
      contains:
        - "# hmmsearch :: search profile(s) against a sequence database"
        - "# target sequence database:"
        - "Internal pipeline statistics summary:"
        - "[ok]"
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_err.log
      md5sum: 538510cfc7483498210f01e53fe035ad
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/prodigal_out.log
      md5sum: 61050b0706addc9498b2088a2d6efa9a
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/.checkpoint
      contains:
        - "Tool: prodigal"
        - "Completed"
        - "jobs"
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
      md5sum: 836e9a80d33d8b89168f07ddc13ee991
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
      md5sum: 836e9a80d33d8b89168f07ddc13ee991
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
      md5sum: 538510cfc7483498210f01e53fe035ad
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
      md5sum: 61050b0706addc9498b2088a2d6efa9a
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/.bbtools_output/.checkpoint
      contains:
        - "Tool: bbtools"
        - "Completed"
        - "jobs"
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/full_table.tsv
      md5sum: 275a7ece09ef61aa59ee7a811289e3d8
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/hmmer_output.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/missing_busco_list.tsv
      md5sum: ab574cde031a3fbff471976ea61e215d
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.json
      contains:
        - "one_line_summary"
        - "mode"
        - "dataset"
    - path: output/busco/test-bacteria_odb10-busco/genome.fna/run_bacteria_odb10/short_summary.txt
      contains:
        - "# BUSCO version is:"
        - "Results:"
        - "busco:"
    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
      contains:
        - "DEBUG:busco.run_BUSCO"
        - "Results from dataset"
        - "how to cite BUSCO"

- name: busco test_busco_eukaryote_metaeuk
  command: nextflow run ./tests/modules/busco -entry test_busco_eukaryote_metaeuk -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
  tags:
    - busco
  files:
    - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.json
      contains:
        - "one_line_summary"
        - "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: ff6d8277e452a83ce9456bbee666feb6
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_err.log
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_out.log
      contains:
        - "IUPAC"
        - "genome scaffold"
        - "Coverage"
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/hmmsearch_err.log
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/hmmsearch_out.log
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run1_err.log
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run1_out.log
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run2_err.log
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/metaeuk_run2_out.log
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/.bbtools_output/.checkpoint
      contains:
        - "Tool: bbtools"
        - "Completed"
        - "jobs"
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/full_table.tsv
      md5sum: ff1b64c2adadcf9f0a954a19893e421b
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/hmmer_output.tar.gz
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/.checkpoint
      contains:
        - "Tool: metaeuk"
        - "Completed"
        - "jobs"
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/combined_pred_proteins.fas
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.codon.fas
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.fas
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.gff
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/initial_results/genome.fasta.headersMap.tsv
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/refseq_db_rerun.faa
      md5sum: d80b8fa4cb5ed0d47d63d6aa93635bc2
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.codon.fas
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.fas
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.gff
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/metaeuk_output/rerun_results/genome.fasta.headersMap.tsv
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/missing_busco_list.tsv
      md5sum: 6c17c7e06991db898b318b932d686406
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/short_summary.json
      contains:
        - "one_line_summary"
        - "mode"
        - "dataset"
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/short_summary.txt
      contains:
        - "# BUSCO version is:"
        - "Results:"
        - "busco:"
    - path: output/busco/test-eukaryota_odb10-busco/logs/busco.log
      contains:
        - "DEBUG:busco.run_BUSCO"
        - "Results from dataset"
        - "how to cite BUSCO"

- name: busco test_busco_eukaryote_augustus
  command: nextflow run ./tests/modules/busco -entry test_busco_eukaryote_augustus -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
  tags:
    - busco
  files:
    - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
      md5sum: cdd3ffd590a778cdd2f0f367ee86eba7
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/.checkpoint
      contains:
        - "Tool: makeblastdb"
        - "Completed"
        - "jobs"
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.ndb
      md5sum: 0d553c830656469211de113c5022f06d
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nhr
      md5sum: 82396da5130a85faf6d454e2889a1d45
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nin
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.njs
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.not
      md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nsq
      md5sum: 4bc119903ac72152363f47612645046a
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.ntf
      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/blast_db/genome.fasta.nto
      md5sum: 33cdeccccebe80329f1fdbee7f5874cb
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_err.log
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/bbtools_out.log
      contains:
        - "IUPAC"
        - "genome scaffold"
        - "Coverage"
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/makeblastdb_err.log
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/makeblastdb_out.log
      contains:
        - "Building a new DB"
        - "Adding sequences from FASTA"
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/tblastn_err.log
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/logs/tblastn_out.log
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/.bbtools_output/.checkpoint
      contains:
        - "Tool: bbtools"
        - "Completed"
        - "jobs"
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/.checkpoint
      contains:
        - "Tool: tblastn"
        - "Completed"
        - "jobs"
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/coordinates.tsv
    - path: output/busco/test-eukaryota_odb10-busco/genome.fasta/run_eukaryota_odb10/blast_output/tblastn.tsv
      contains:
        - "TBLASTN"
        - "BLAST processed"
        - "queries"
    - path: output/busco/test-eukaryota_odb10-busco/logs/busco.log
      contains:
        - "DEBUG:busco.run_BUSCO"
        - "Running Augustus gene predictor"

- name: busco test_busco_protein
  command: nextflow run ./tests/modules/busco -entry test_busco_protein -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
  tags:
    - busco
  files:
    - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.json
      contains:
        - "one_line_summary"
        - "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: 7a65e6cbb6c56a2ea4e739ae0aa3297d
    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
      contains:
        - "DEBUG:busco.run_BUSCO"
        - "Results from dataset"
        - "how to cite BUSCO"
    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/logs/hmmsearch_err.log
    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/logs/hmmsearch_out.log
      contains:
        - "# hmmsearch :: search profile(s) against a sequence database"
        - "# target sequence database:"
        - "Internal pipeline statistics summary:"
        - "[ok]"
    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/full_table.tsv
      md5sum: 81e0e9a5897bb72fffbb1866779f6834
    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/hmmer_output.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/missing_busco_list.tsv
      md5sum: 8e6b6a4ba25caf8e7ad15e8a77064755
    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/short_summary.json
      contains:
        - "one_line_summary"
        - "mode"
        - "dataset"
    - path: output/busco/test-bacteria_odb10-busco/proteome.fasta/run_bacteria_odb10/short_summary.txt
      contains:
        - "# BUSCO version is:"
        - "Results:"
        - "busco:"

- name: busco test_busco_transcriptome
  command: nextflow run ./tests/modules/busco -entry test_busco_transcriptome -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config
  tags:
    - busco
  files:
    - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
      contains:
        - "one_line_summary"
        - "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: 46118ecf60d1b87d22b96d80f4f03632
    - path: output/busco/test-bacteria_odb10-busco/logs/busco.log
      contains:
        - "DEBUG:busco.run_BUSCO"
        - "Results from dataset"
        - "how to cite BUSCO"
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/.checkpoint
      contains:
        - "Tool: makeblastdb"
        - "Completed"
        - "jobs"
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.ndb
      md5sum: 3788c017fe5e6f0f58224e9cdd21822b
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nhr
      md5sum: 8ecd2ce392bb5e25ddbe1d85f879582e
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nin
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.njs
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.not
      md5sum: 0c340e376c7e85d19f82ec1a833e6a6e
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nsq
      md5sum: 532d5c0a7ea00fe95ca3c97cb3be6198
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.ntf
      md5sum: de1250813f0c7affc6d12dac9d0fb6bb
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/blast_db/test1.contigs.fa.nto
      md5sum: ff74bd41f9cc9b011c63a32c4f7693bf
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/hmmsearch_err.log
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/hmmsearch_out.log
      contains:
        - "# hmmsearch :: search profile(s) against a sequence database"
        - "# target sequence database:"
        - "Internal pipeline statistics summary:"
        - "[ok]"
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/makeblastdb_err.log
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/makeblastdb_out.log
      contains:
        - "Building a new DB"
        - "Adding sequences from FASTA"
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/tblastn_err.log
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/logs/tblastn_out.log
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/.checkpoint
      contains:
        - "Tool: tblastn"
        - "Completed"
        - "jobs"
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/coordinates.tsv
      md5sum: cc30eed321944af293452bdbcfc24292
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_101.temp
      md5sum: 73e9c65fc83fedc58f57f09b08f08238
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_119.temp
      md5sum: 7fa4cc7955ec0cc36330a221c579b975
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_129.temp
      md5sum: 6f1601c875d019e3f6f1f98ed8e988d4
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_138.temp
      md5sum: 3f8e034686cd240c2330650d791bcae2
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_143.temp
      md5sum: df3dfa8e9ba30ed70cf75b5e7abf2179
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_172.temp
      md5sum: 7d463e0e6cf7169bc9077d8dc776dda1
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_178.temp
      md5sum: 2288edf7fa4f88f51b4cf4d94086f77e
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_188.temp
      md5sum: 029906abbad6d87fc57830dd548cac24
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_195.temp
      md5sum: 4937f3b348774a31b1160a00297c29cc
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_210.temp
      md5sum: afcb20ba4c466479d6b91c8c62251e1f
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_232.temp
      md5sum: 2e1e823ce017345bd998191a39fa9924
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_268.temp
      md5sum: 08c2d82c34ecffbe1c638b410349412e
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_29.temp
      md5sum: cd9b63cf93524284781535c888313764
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_44.temp
      md5sum: d1929b742b24ebe379bf4801ca882dca
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_58.temp
      md5sum: 69215765b010c05336538cb322c900b3
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_72.temp
      md5sum: 6feaa1cc3b0899a147ea9d466878f3e3
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_80.temp
      md5sum: 13625eae14e860a96ce17cd4e37e9d01
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_81.temp
      md5sum: e14b2484649b0dbc8926815c207b806d
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_93.temp
      md5sum: 6902c93691df00e690faea914c71839e
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/sequences/k141_97.temp
      md5sum: 0a0d9d38a83acbd5ad43c29cdf429988
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/blast_output/tblastn.tsv
      contains:
        - "TBLASTN"
        - "BLAST processed"
        - "queries"
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/full_table.tsv
      md5sum: 14bb2d7788bd0aa547e4a99df6659f1e
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/hmmer_output.tar.gz
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/missing_busco_list.tsv
      md5sum: 485902b7b62403985ee9f781e17b20ab
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/short_summary.json
      contains:
        - "one_line_summary"
        - "mode"
        - "dataset"
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/short_summary.txt
      contains:
        - "# BUSCO version is:"
        - "Results:"
        - "busco:"
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/run_bacteria_odb10/single_copy_proteins.faa
      md5sum: e04b9465733577ae6e4bccb7aa01e720
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1024388at2.faa
      md5sum: 7333c39a20258f20c7019ea0cd83157c
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1054741at2.faa
      md5sum: ebb481e77a824685fbe04d8a2f3a0d7d
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1093223at2.faa
      md5sum: 34621c7d499034e8f8e6b92fd4020a93
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1151822at2.faa
      md5sum: aa89ca381c1c70c9c4e1380351ca7c2a
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/143460at2.faa
      md5sum: f2e91d78b8dd3722840378789f29e8c8
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1491686at2.faa
      md5sum: 73c25aef5c9cba7f4151804941b146ea
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1504821at2.faa
      md5sum: cda556018d1f84ebe517e89f6fc107d0
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1574817at2.faa
      md5sum: a9096c9fb8b25c78a72871ab0463acdc
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1592033at2.faa
      md5sum: e463d25ce186c0cebfd749474f3a4c64
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1623045at2.faa
      md5sum: f2cfd241590c6d8377286d6135480937
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1661836at2.faa
      md5sum: 586569546fb9861502468e3d9ba2775c
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1674344at2.faa
      md5sum: 24c658bee14ad84b062d81ad96642eb8
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1698718at2.faa
      md5sum: 0b8e26ddf5149bbd8805be7af125208d
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/1990650at2.faa
      md5sum: 159320712ee01fb2ccb31a25df44eead
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/223233at2.faa
      md5sum: 812629c0b06ac3d18661c2ca78de0c08
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/402899at2.faa
      md5sum: f7ff4e1591342d30b77392a2e84b57d9
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/505485at2.faa
      md5sum: 7b34a24fc49c540d46fcf96ff5129564
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/665824at2.faa
      md5sum: 4cff2df64f6bcaff8bc19c234c8bcccd
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/776861at2.faa
      md5sum: 613af7a3fea30ea2bece66f603b9284a
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/874197at2.faa
      md5sum: a7cd1b13c9ef91c7ef4e31614166f197
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/932854at2.faa
      md5sum: fe313ffd5efdb0fed887a04fba352552
    - path: output/busco/test-bacteria_odb10-busco/test1.contigs.fa/translated_proteins/95696at2.faa
      md5sum: 4e1f30a2fea4dfbf9bb7fae2700622a0