From 73a8df9522e31eaa34f9f611d8a5a42d6a8c53fe Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Wed, 4 May 2022 11:52:42 +0000 Subject: [PATCH] Fix no genes found test and update test.yml --- modules/busco/main.nf | 6 +- tests/modules/busco/main.nf | 166 +++++++++++++++++------------------ tests/modules/busco/test.yml | 126 +++++++++++++++++++++++--- 3 files changed, 198 insertions(+), 100 deletions(-) diff --git a/modules/busco/main.nf b/modules/busco/main.nf index 59ac20f8..f6bd63e2 100644 --- a/modules/busco/main.nf +++ b/modules/busco/main.nf @@ -15,8 +15,8 @@ process BUSCO { output: tuple val(meta), path("*-busco.batch_summary.txt"), emit: batch_summary - tuple val(meta), path("short_summary.*.txt") , emit: short_summaries_txt - tuple val(meta), path("short_summary.*.json") , emit: short_summaries_json + tuple val(meta), path("short_summary.*.txt") , emit: short_summaries_txt, optional: true + tuple val(meta), path("short_summary.*.json") , emit: short_summaries_json, optional: true tuple val(meta), path("*-busco") , emit: busco_dir path "versions.yml" , emit: versions @@ -73,7 +73,7 @@ process BUSCO { # Move files to avoid staging/publishing issues mv ${prefix}-busco/batch_summary.txt ${prefix}-busco.batch_summary.txt - mv ${prefix}-busco/*/short_summary.*.{json,txt} . + mv ${prefix}-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found." cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/tests/modules/busco/main.nf b/tests/modules/busco/main.nf index a678d371..f0201d21 100644 --- a/tests/modules/busco/main.nf +++ b/tests/modules/busco/main.nf @@ -20,9 +20,12 @@ workflow test_busco_genome_single_fasta { ) /* Output tree: - /tmp/tmpimsfk4sj/busco/ - ├── test-bacteria_odb10-busco -> /tmp/tmp1sz7013h/b7/fdeaab567e1c5bccc475a4c19b8582/test-bacteria_odb10-busco/ - │ ├── batch_summary.txt + /tmp/tmpisa3ktco/busco/ + ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/short_summary.specific.bacteria_odb10.genome.fna.json + ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/short_summary.specific.bacteria_odb10.genome.fna.txt + ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/short_summary.specific.bacteroidetes_odb10.genome.fna.json + ├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/short_summary.specific.bacteroidetes_odb10.genome.fna.txt + ├── test-bacteria_odb10-busco -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/test-bacteria_odb10-busco/ │ ├── genome.fna/ │ │ ├── logs/ │ │ │ ├── hmmsearch_err.log @@ -31,19 +34,17 @@ workflow test_busco_genome_single_fasta { │ │ │ └── prodigal_out.log │ │ ├── prodigal_output/ │ │ │ └── predicted_genes/ - │ │ ├── run_bacteria_odb10/ - │ │ │ ├── busco_sequences/ - │ │ │ ├── full_table.tsv - │ │ │ ├── hmmer_output/ - │ │ │ ├── missing_busco_list.tsv - │ │ │ ├── short_summary.json - │ │ │ └── short_summary.txt - │ │ ├── short_summary.specific.bacteria_odb10.genome.fna.json - │ │ └── short_summary.specific.bacteria_odb10.genome.fna.txt + │ │ └── run_bacteria_odb10/ + │ │ ├── busco_sequences/ + │ │ ├── full_table.tsv + │ │ ├── hmmer_output/ + │ │ ├── missing_busco_list.tsv + │ │ ├── short_summary.json + │ │ └── short_summary.txt │ └── logs/ │ └── busco.log - ├── test-bacteroidetes_odb10-busco -> /tmp/tmp1sz7013h/75/0da56f59ee44bd2b85e0172906de49/test-bacteroidetes_odb10-busco/ - │ ├── batch_summary.txt + ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/test-bacteria_odb10-busco.batch_summary.txt + ├── test-bacteroidetes_odb10-busco -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/test-bacteroidetes_odb10-busco/ │ ├── genome.fna/ │ │ ├── logs/ │ │ │ ├── hmmsearch_err.log @@ -52,18 +53,17 @@ workflow test_busco_genome_single_fasta { │ │ │ └── prodigal_out.log │ │ ├── prodigal_output/ │ │ │ └── predicted_genes/ - │ │ ├── run_bacteroidetes_odb10/ - │ │ │ ├── busco_sequences/ - │ │ │ ├── full_table.tsv - │ │ │ ├── hmmer_output/ - │ │ │ ├── missing_busco_list.tsv - │ │ │ ├── short_summary.json - │ │ │ └── short_summary.txt - │ │ ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json - │ │ └── short_summary.specific.bacteroidetes_odb10.genome.fna.txt + │ │ └── run_bacteroidetes_odb10/ + │ │ ├── busco_sequences/ + │ │ ├── full_table.tsv + │ │ ├── hmmer_output/ + │ │ ├── missing_busco_list.tsv + │ │ ├── short_summary.json + │ │ └── short_summary.txt │ └── logs/ │ └── busco.log - └── versions.yml -> /tmp/tmp1sz7013h/b7/fdeaab567e1c5bccc475a4c19b8582/versions.yml + ├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/test-bacteroidetes_odb10-busco.batch_summary.txt + └── versions.yml -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/versions.yml */ } @@ -86,9 +86,12 @@ workflow test_busco_genome_multi_fasta { ) /* Output tree: - /tmp/tmpt22rjxzq/busco/ - ├── test-bacteria_odb10-busco -> /tmp/tmpfxt64xr_/36/425acbe5e9b27ba0bac8861f735494/test-bacteria_odb10-busco/ - │ ├── batch_summary.txt + /tmp/tmpk19byek7/busco/ + ├── short_summary.specific.bacteria_odb10.genome.fasta.json -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fasta.json + ├── short_summary.specific.bacteria_odb10.genome.fasta.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fasta.txt + ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fna.json + ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fna.txt + ├── test-bacteria_odb10-busco -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/test-bacteria_odb10-busco/ │ ├── genome.fasta/ │ │ ├── logs/ │ │ │ ├── hmmsearch_err.log @@ -97,15 +100,13 @@ workflow test_busco_genome_multi_fasta { │ │ │ └── prodigal_out.log │ │ ├── prodigal_output/ │ │ │ └── predicted_genes/ - │ │ ├── run_bacteria_odb10/ - │ │ │ ├── busco_sequences/ - │ │ │ ├── full_table.tsv - │ │ │ ├── hmmer_output/ - │ │ │ ├── missing_busco_list.tsv - │ │ │ ├── short_summary.json - │ │ │ └── short_summary.txt - │ │ ├── short_summary.specific.bacteria_odb10.genome.fasta.json - │ │ └── short_summary.specific.bacteria_odb10.genome.fasta.txt + │ │ └── run_bacteria_odb10/ + │ │ ├── busco_sequences/ + │ │ ├── full_table.tsv + │ │ ├── hmmer_output/ + │ │ ├── missing_busco_list.tsv + │ │ ├── short_summary.json + │ │ └── short_summary.txt │ ├── genome.fna/ │ │ ├── logs/ │ │ │ ├── hmmsearch_err.log @@ -114,18 +115,17 @@ workflow test_busco_genome_multi_fasta { │ │ │ └── prodigal_out.log │ │ ├── prodigal_output/ │ │ │ └── predicted_genes/ - │ │ ├── run_bacteria_odb10/ - │ │ │ ├── busco_sequences/ - │ │ │ ├── full_table.tsv - │ │ │ ├── hmmer_output/ - │ │ │ ├── missing_busco_list.tsv - │ │ │ ├── short_summary.json - │ │ │ └── short_summary.txt - │ │ ├── short_summary.specific.bacteria_odb10.genome.fna.json - │ │ └── short_summary.specific.bacteria_odb10.genome.fna.txt + │ │ └── run_bacteria_odb10/ + │ │ ├── busco_sequences/ + │ │ ├── full_table.tsv + │ │ ├── hmmer_output/ + │ │ ├── missing_busco_list.tsv + │ │ ├── short_summary.json + │ │ └── short_summary.txt │ └── logs/ │ └── busco.log - └── versions.yml -> /tmp/tmpfxt64xr_/36/425acbe5e9b27ba0bac8861f735494/versions.yml + ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/test-bacteria_odb10-busco.batch_summary.txt + └── versions.yml -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/versions.yml */ } @@ -145,28 +145,28 @@ workflow test_busco_eukaryote_metaeuk { ) /* Output tree: - /tmp/tmp22sf7kg9/busco/ - ├── test-eukaryota_odb10-busco -> /tmp/tmpmic8qsk6/d5/d8cb6681c0fcaa6da34b57ec174d59/test-eukaryota_odb10-busco/ - │ ├── batch_summary.txt + /tmp/tmpeq4dsir5/busco/ + ├── short_summary.specific.eukaryota_odb10.genome.fasta.json -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/short_summary.specific.eukaryota_odb10.genome.fasta.json + ├── short_summary.specific.eukaryota_odb10.genome.fasta.txt -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/short_summary.specific.eukaryota_odb10.genome.fasta.txt + ├── test-eukaryota_odb10-busco -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/test-eukaryota_odb10-busco/ │ ├── genome.fasta/ │ │ ├── logs/ │ │ │ ├── hmmsearch_err.log │ │ │ ├── hmmsearch_out.log │ │ │ ├── metaeuk_err.log │ │ │ └── metaeuk_out.log - │ │ ├── run_eukaryota_odb10/ - │ │ │ ├── busco_sequences/ - │ │ │ ├── full_table.tsv - │ │ │ ├── hmmer_output/ - │ │ │ ├── metaeuk_output/ - │ │ │ ├── missing_busco_list.tsv - │ │ │ ├── short_summary.json - │ │ │ └── short_summary.txt - │ │ ├── short_summary.specific.eukaryota_odb10.genome.fasta.json - │ │ └── short_summary.specific.eukaryota_odb10.genome.fasta.txt + │ │ └── run_eukaryota_odb10/ + │ │ ├── busco_sequences/ + │ │ ├── full_table.tsv + │ │ ├── hmmer_output/ + │ │ ├── metaeuk_output/ + │ │ ├── missing_busco_list.tsv + │ │ ├── short_summary.json + │ │ └── short_summary.txt │ └── logs/ │ └── busco.log - └── versions.yml -> /tmp/tmpmic8qsk6/d5/d8cb6681c0fcaa6da34b57ec174d59/versions.yml + ├── test-eukaryota_odb10-busco.batch_summary.txt -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/test-eukaryota_odb10-busco.batch_summary.txt + └── versions.yml -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/versions.yml */ } @@ -186,9 +186,8 @@ workflow test_busco_eukaryote_augustus { ) /* Output tree: - /tmp/tmpo77wyvb9/busco/ - ├── test-eukaryota_odb10-busco -> /tmp/tmpshljnwcg/25/9891a19cbabda15a5c10fb5e34987f/test-eukaryota_odb10-busco/ - │ ├── batch_summary.txt + /tmp/tmp2xqaygjj/busco/ + ├── test-eukaryota_odb10-busco -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/test-eukaryota_odb10-busco/ │ ├── genome.fasta/ │ │ ├── blast_db/ │ │ │ ├── genome.fasta.ndb @@ -210,7 +209,8 @@ workflow test_busco_eukaryote_augustus { │ │ └── hmmer_output/ │ └── logs/ │ └── busco.log - └── versions.yml -> /tmp/tmpshljnwcg/25/9891a19cbabda15a5c10fb5e34987f/versions.yml + ├── test-eukaryota_odb10-busco.batch_summary.txt -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/test-eukaryota_odb10-busco.batch_summary.txt + └── versions.yml -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/versions.yml */ } @@ -230,25 +230,25 @@ workflow test_busco_protein { ) /* Output tree: - /tmp/tmplju98s42/busco/ - ├── test-bacteria_odb10-busco -> /tmp/tmp0oru9_61/9c/e992f5eee84806770002e4510f51cb/test-bacteria_odb10-busco/ - │ ├── batch_summary.txt + /tmp/tmpzwd5dn56/busco/ + ├── short_summary.specific.bacteria_odb10.proteome.fasta.json -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/short_summary.specific.bacteria_odb10.proteome.fasta.json + ├── short_summary.specific.bacteria_odb10.proteome.fasta.txt -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/short_summary.specific.bacteria_odb10.proteome.fasta.txt + ├── test-bacteria_odb10-busco -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/test-bacteria_odb10-busco/ │ ├── logs/ │ │ └── busco.log │ └── proteome.fasta/ │ ├── logs/ │ │ ├── hmmsearch_err.log │ │ └── hmmsearch_out.log - │ ├── run_bacteria_odb10/ - │ │ ├── busco_sequences/ - │ │ ├── full_table.tsv - │ │ ├── hmmer_output/ - │ │ ├── missing_busco_list.tsv - │ │ ├── short_summary.json - │ │ └── short_summary.txt - │ ├── short_summary.specific.bacteria_odb10.proteome.fasta.json - │ └── short_summary.specific.bacteria_odb10.proteome.fasta.txt - └── versions.yml -> /tmp/tmp0oru9_61/9c/e992f5eee84806770002e4510f51cb/versions.yml + │ └── run_bacteria_odb10/ + │ ├── busco_sequences/ + │ ├── full_table.tsv + │ ├── hmmer_output/ + │ ├── missing_busco_list.tsv + │ ├── short_summary.json + │ └── short_summary.txt + ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/test-bacteria_odb10-busco.batch_summary.txt + └── versions.yml -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/versions.yml */ } workflow test_busco_transcriptome { @@ -266,9 +266,10 @@ workflow test_busco_transcriptome { ) /* Output tree: - /tmp/tmp5twpr8o9/busco/ - ├── test-bacteria_odb10-busco -> /tmp/tmp_qyjiads/0d/886515d0f06686b2227517398ef8ce/test-bacteria_odb10-busco/ - │ ├── batch_summary.txt + /tmp/tmpitjyvo9g/busco/ + ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.json -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/short_summary.specific.bacteria_odb10.test1.contigs.fa.json + ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.txt -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt + ├── test-bacteria_odb10-busco -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/test-bacteria_odb10-busco/ │ ├── logs/ │ │ └── busco.log │ └── test1.contigs.fa/ @@ -296,8 +297,6 @@ workflow test_busco_transcriptome { │ │ ├── short_summary.json │ │ ├── short_summary.txt │ │ └── single_copy_proteins.faa - │ ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.json - │ ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.txt │ └── translated_proteins/ │ ├── 1024388at2.faa │ ├── 1054741at2.faa @@ -321,7 +320,8 @@ workflow test_busco_transcriptome { │ ├── 874197at2.faa │ ├── 932854at2.faa │ └── 95696at2.faa - └── versions.yml -> /tmp/tmp_qyjiads/0d/886515d0f06686b2227517398ef8ce/versions.yml + ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/test-bacteria_odb10-busco.batch_summary.txt + └── versions.yml -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/versions.yml */ } diff --git a/tests/modules/busco/test.yml b/tests/modules/busco/test.yml index 2125c3a4..b838d9b7 100644 --- a/tests/modules/busco/test.yml +++ b/tests/modules/busco/test.yml @@ -2,9 +2,39 @@ command: nextflow run tests/modules/busco -entry test_busco_genome_single_fasta -c tests/config/nextflow.config tags: - busco - - bacteria - - genome 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 @@ -12,9 +42,37 @@ command: nextflow run tests/modules/busco -entry test_busco_genome_multi_fasta -c tests/config/nextflow.config tags: - busco - - bacteria - - genome 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 + md5sum: 5360dfe83bec1f5741ee115e53e6b517 - path: output/busco/versions.yml md5sum: 9a959eb0a1f765777dff1ea2f5c139c0 @@ -22,10 +80,23 @@ command: nextflow run tests/modules/busco -entry test_busco_eukaryote_metaeuk -c tests/config/nextflow.config tags: - busco - - eukaryote - - genome - - metaeuk 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 @@ -33,10 +104,9 @@ command: nextflow run tests/modules/busco -entry test_busco_eukaryote_augustus -c tests/config/nextflow.config tags: - busco - - eukaryote - - genome - - augustus files: + - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt + md5sum: 660393dd43cd6a093b952d4b8ad41e40 - path: output/busco/versions.yml md5sum: 2caac915461410b16a1524ac064cd0df @@ -44,9 +114,23 @@ command: nextflow run tests/modules/busco -entry test_busco_protein -c tests/config/nextflow.config tags: - busco - - bacteria - - proteins 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 @@ -54,8 +138,22 @@ command: nextflow run tests/modules/busco -entry test_busco_transcriptome -c tests/config/nextflow.config tags: - busco - - bacteria - - transcriptome 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