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Fix no genes found test and update test.yml

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This commit is contained in:
Mahesh Binzer-Panchal 2022-05-04 11:52:42 +00:00
parent 8df20218bf
commit 73a8df9522
3 changed files with 198 additions and 100 deletions
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6
modules/busco/main.nf
View file

@ -15,8 +15,8 @@ process BUSCO {
output: output:
tuple val(meta), path("*-busco.batch_summary.txt"), emit: batch_summary 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.*.txt") , emit: short_summaries_txt, optional: true
tuple val(meta), path("short_summary.*.json") , emit: short_summaries_json tuple val(meta), path("short_summary.*.json") , emit: short_summaries_json, optional: true
tuple val(meta), path("*-busco") , emit: busco_dir tuple val(meta), path("*-busco") , emit: busco_dir
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
@ -73,7 +73,7 @@ process BUSCO {
# Move files to avoid staging/publishing issues # Move files to avoid staging/publishing issues
mv ${prefix}-busco/batch_summary.txt ${prefix}-busco.batch_summary.txt mv ${prefix}-busco/batch_summary.txt ${prefix}-busco.batch_summary.txt
mv ${prefix}-busco/*/short_summary.*.{json,txt} . mv ${prefix}-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found."
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

166
tests/modules/busco/main.nf
View file

@ -20,9 +20,12 @@ workflow test_busco_genome_single_fasta {
) )
/* Output tree: /* Output tree:
/tmp/tmpimsfk4sj/busco/ /tmp/tmpisa3ktco/busco/
├── test-bacteria_odb10-busco -> /tmp/tmp1sz7013h/b7/fdeaab567e1c5bccc475a4c19b8582/test-bacteria_odb10-busco/ ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/short_summary.specific.bacteria_odb10.genome.fna.json
│ ├── batch_summary.txt ├── 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/ │ ├── genome.fna/
│ │ ├── logs/ │ │ ├── logs/
│ │ │ ├── hmmsearch_err.log │ │ │ ├── hmmsearch_err.log
@ -31,19 +34,17 @@ workflow test_busco_genome_single_fasta {
│ │ │ └── prodigal_out.log │ │ │ └── prodigal_out.log
│ │ ├── prodigal_output/ │ │ ├── prodigal_output/
│ │ │ └── predicted_genes/ │ │ │ └── predicted_genes/
│ │ ├── run_bacteria_odb10/ │ │ └── run_bacteria_odb10/
│ │ │ ├── busco_sequences/ │ │ ├── busco_sequences/
│ │ │ ├── full_table.tsv │ │ ├── full_table.tsv
│ │ │ ├── hmmer_output/ │ │ ├── hmmer_output/
│ │ │ ├── missing_busco_list.tsv │ │ ├── missing_busco_list.tsv
│ │ │ ├── short_summary.json │ │ ├── short_summary.json
│ │ │ └── short_summary.txt │ │ └── short_summary.txt
│ │ ├── short_summary.specific.bacteria_odb10.genome.fna.json
│ │ └── short_summary.specific.bacteria_odb10.genome.fna.txt
│ └── logs/ │ └── logs/
│ └── busco.log │ └── busco.log
├── test-bacteroidetes_odb10-busco -> /tmp/tmp1sz7013h/75/0da56f59ee44bd2b85e0172906de49/test-bacteroidetes_odb10-busco/ ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/test-bacteria_odb10-busco.batch_summary.txt
│ ├── batch_summary.txt ├── test-bacteroidetes_odb10-busco -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/test-bacteroidetes_odb10-busco/
│ ├── genome.fna/ │ ├── genome.fna/
│ │ ├── logs/ │ │ ├── logs/
│ │ │ ├── hmmsearch_err.log │ │ │ ├── hmmsearch_err.log
@ -52,18 +53,17 @@ workflow test_busco_genome_single_fasta {
│ │ │ └── prodigal_out.log │ │ │ └── prodigal_out.log
│ │ ├── prodigal_output/ │ │ ├── prodigal_output/
│ │ │ └── predicted_genes/ │ │ │ └── predicted_genes/
│ │ ├── run_bacteroidetes_odb10/ │ │ └── run_bacteroidetes_odb10/
│ │ │ ├── busco_sequences/ │ │ ├── busco_sequences/
│ │ │ ├── full_table.tsv │ │ ├── full_table.tsv
│ │ │ ├── hmmer_output/ │ │ ├── hmmer_output/
│ │ │ ├── missing_busco_list.tsv │ │ ├── missing_busco_list.tsv
│ │ │ ├── short_summary.json │ │ ├── short_summary.json
│ │ │ └── short_summary.txt │ │ └── short_summary.txt
│ │ ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json
│ │ └── short_summary.specific.bacteroidetes_odb10.genome.fna.txt
│ └── logs/ │ └── logs/
│ └── busco.log │ └── 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: /* Output tree:
/tmp/tmpt22rjxzq/busco/ /tmp/tmpk19byek7/busco/
├── test-bacteria_odb10-busco -> /tmp/tmpfxt64xr_/36/425acbe5e9b27ba0bac8861f735494/test-bacteria_odb10-busco/ ├── short_summary.specific.bacteria_odb10.genome.fasta.json -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fasta.json
│ ├── batch_summary.txt ├── 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/ │ ├── genome.fasta/
│ │ ├── logs/ │ │ ├── logs/
│ │ │ ├── hmmsearch_err.log │ │ │ ├── hmmsearch_err.log
@ -97,15 +100,13 @@ workflow test_busco_genome_multi_fasta {
│ │ │ └── prodigal_out.log │ │ │ └── prodigal_out.log
│ │ ├── prodigal_output/ │ │ ├── prodigal_output/
│ │ │ └── predicted_genes/ │ │ │ └── predicted_genes/
│ │ ├── run_bacteria_odb10/ │ │ └── run_bacteria_odb10/
│ │ │ ├── busco_sequences/ │ │ ├── busco_sequences/
│ │ │ ├── full_table.tsv │ │ ├── full_table.tsv
│ │ │ ├── hmmer_output/ │ │ ├── hmmer_output/
│ │ │ ├── missing_busco_list.tsv │ │ ├── missing_busco_list.tsv
│ │ │ ├── short_summary.json │ │ ├── short_summary.json
│ │ │ └── short_summary.txt │ │ └── short_summary.txt
│ │ ├── short_summary.specific.bacteria_odb10.genome.fasta.json
│ │ └── short_summary.specific.bacteria_odb10.genome.fasta.txt
│ ├── genome.fna/ │ ├── genome.fna/
│ │ ├── logs/ │ │ ├── logs/
│ │ │ ├── hmmsearch_err.log │ │ │ ├── hmmsearch_err.log
@ -114,18 +115,17 @@ workflow test_busco_genome_multi_fasta {
│ │ │ └── prodigal_out.log │ │ │ └── prodigal_out.log
│ │ ├── prodigal_output/ │ │ ├── prodigal_output/
│ │ │ └── predicted_genes/ │ │ │ └── predicted_genes/
│ │ ├── run_bacteria_odb10/ │ │ └── run_bacteria_odb10/
│ │ │ ├── busco_sequences/ │ │ ├── busco_sequences/
│ │ │ ├── full_table.tsv │ │ ├── full_table.tsv
│ │ │ ├── hmmer_output/ │ │ ├── hmmer_output/
│ │ │ ├── missing_busco_list.tsv │ │ ├── missing_busco_list.tsv
│ │ │ ├── short_summary.json │ │ ├── short_summary.json
│ │ │ └── short_summary.txt │ │ └── short_summary.txt
│ │ ├── short_summary.specific.bacteria_odb10.genome.fna.json
│ │ └── short_summary.specific.bacteria_odb10.genome.fna.txt
│ └── logs/ │ └── logs/
│ └── busco.log │ └── 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: /* Output tree:
/tmp/tmp22sf7kg9/busco/ /tmp/tmpeq4dsir5/busco/
├── test-eukaryota_odb10-busco -> /tmp/tmpmic8qsk6/d5/d8cb6681c0fcaa6da34b57ec174d59/test-eukaryota_odb10-busco/ ├── short_summary.specific.eukaryota_odb10.genome.fasta.json -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/short_summary.specific.eukaryota_odb10.genome.fasta.json
│ ├── batch_summary.txt ├── 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/ │ ├── genome.fasta/
│ │ ├── logs/ │ │ ├── logs/
│ │ │ ├── hmmsearch_err.log │ │ │ ├── hmmsearch_err.log
│ │ │ ├── hmmsearch_out.log │ │ │ ├── hmmsearch_out.log
│ │ │ ├── metaeuk_err.log │ │ │ ├── metaeuk_err.log
│ │ │ └── metaeuk_out.log │ │ │ └── metaeuk_out.log
│ │ ├── run_eukaryota_odb10/ │ │ └── run_eukaryota_odb10/
│ │ │ ├── busco_sequences/ │ │ ├── busco_sequences/
│ │ │ ├── full_table.tsv │ │ ├── full_table.tsv
│ │ │ ├── hmmer_output/ │ │ ├── hmmer_output/
│ │ │ ├── metaeuk_output/ │ │ ├── metaeuk_output/
│ │ │ ├── missing_busco_list.tsv │ │ ├── missing_busco_list.tsv
│ │ │ ├── short_summary.json │ │ ├── short_summary.json
│ │ │ └── short_summary.txt │ │ └── short_summary.txt
│ │ ├── short_summary.specific.eukaryota_odb10.genome.fasta.json
│ │ └── short_summary.specific.eukaryota_odb10.genome.fasta.txt
│ └── logs/ │ └── logs/
│ └── busco.log │ └── 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: /* Output tree:
/tmp/tmpo77wyvb9/busco/ /tmp/tmp2xqaygjj/busco/
├── test-eukaryota_odb10-busco -> /tmp/tmpshljnwcg/25/9891a19cbabda15a5c10fb5e34987f/test-eukaryota_odb10-busco/ ├── test-eukaryota_odb10-busco -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/test-eukaryota_odb10-busco/
│ ├── batch_summary.txt
│ ├── genome.fasta/ │ ├── genome.fasta/
│ │ ├── blast_db/ │ │ ├── blast_db/
│ │ │ ├── genome.fasta.ndb │ │ │ ├── genome.fasta.ndb
@ -210,7 +209,8 @@ workflow test_busco_eukaryote_augustus {
│ │ └── hmmer_output/ │ │ └── hmmer_output/
│ └── logs/ │ └── logs/
│ └── busco.log │ └── 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: /* Output tree:
/tmp/tmplju98s42/busco/ /tmp/tmpzwd5dn56/busco/
├── test-bacteria_odb10-busco -> /tmp/tmp0oru9_61/9c/e992f5eee84806770002e4510f51cb/test-bacteria_odb10-busco/ ├── short_summary.specific.bacteria_odb10.proteome.fasta.json -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/short_summary.specific.bacteria_odb10.proteome.fasta.json
│ ├── batch_summary.txt ├── 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/ │ ├── logs/
│ │ └── busco.log │ │ └── busco.log
│ └── proteome.fasta/ │ └── proteome.fasta/
│ ├── logs/ │ ├── logs/
│ │ ├── hmmsearch_err.log │ │ ├── hmmsearch_err.log
│ │ └── hmmsearch_out.log │ │ └── hmmsearch_out.log
│ ├── run_bacteria_odb10/ │ └── run_bacteria_odb10/
│ │ ├── busco_sequences/ │ ├── busco_sequences/
│ │ ├── full_table.tsv │ ├── full_table.tsv
│ │ ├── hmmer_output/ │ ├── hmmer_output/
│ │ ├── missing_busco_list.tsv │ ├── missing_busco_list.tsv
│ │ ├── short_summary.json │ ├── short_summary.json
│ │ └── short_summary.txt │ └── short_summary.txt
│ ├── short_summary.specific.bacteria_odb10.proteome.fasta.json ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/test-bacteria_odb10-busco.batch_summary.txt
│ └── short_summary.specific.bacteria_odb10.proteome.fasta.txt └── versions.yml -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/versions.yml
└── versions.yml -> /tmp/tmp0oru9_61/9c/e992f5eee84806770002e4510f51cb/versions.yml
*/ */
} }
workflow test_busco_transcriptome { workflow test_busco_transcriptome {
@ -266,9 +266,10 @@ workflow test_busco_transcriptome {
) )
/* Output tree: /* Output tree:
/tmp/tmp5twpr8o9/busco/ /tmp/tmpitjyvo9g/busco/
├── test-bacteria_odb10-busco -> /tmp/tmp_qyjiads/0d/886515d0f06686b2227517398ef8ce/test-bacteria_odb10-busco/ ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.json -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
│ ├── batch_summary.txt ├── 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/ │ ├── logs/
│ │ └── busco.log │ │ └── busco.log
│ └── test1.contigs.fa/ │ └── test1.contigs.fa/
@ -296,8 +297,6 @@ workflow test_busco_transcriptome {
│ │ ├── short_summary.json │ │ ├── short_summary.json
│ │ ├── short_summary.txt │ │ ├── short_summary.txt
│ │ └── single_copy_proteins.faa │ │ └── single_copy_proteins.faa
│ ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.json
│ ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
│ └── translated_proteins/ │ └── translated_proteins/
│ ├── 1024388at2.faa │ ├── 1024388at2.faa
│ ├── 1054741at2.faa │ ├── 1054741at2.faa
@ -321,7 +320,8 @@ workflow test_busco_transcriptome {
│ ├── 874197at2.faa │ ├── 874197at2.faa
│ ├── 932854at2.faa │ ├── 932854at2.faa
│ └── 95696at2.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
*/ */
} }

126
tests/modules/busco/test.yml
View file

@ -2,9 +2,39 @@
command: nextflow run tests/modules/busco -entry test_busco_genome_single_fasta -c tests/config/nextflow.config command: nextflow run tests/modules/busco -entry test_busco_genome_single_fasta -c tests/config/nextflow.config
tags: tags:
- busco - busco
- bacteria
- genome
files: 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 - path: output/busco/versions.yml
md5sum: 8aa830f71587d859df35c6cfab59f35d md5sum: 8aa830f71587d859df35c6cfab59f35d
@ -12,9 +42,37 @@
command: nextflow run tests/modules/busco -entry test_busco_genome_multi_fasta -c tests/config/nextflow.config command: nextflow run tests/modules/busco -entry test_busco_genome_multi_fasta -c tests/config/nextflow.config
tags: tags:
- busco - busco
- bacteria
- genome
files: 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 - path: output/busco/versions.yml
md5sum: 9a959eb0a1f765777dff1ea2f5c139c0 md5sum: 9a959eb0a1f765777dff1ea2f5c139c0
@ -22,10 +80,23 @@
command: nextflow run tests/modules/busco -entry test_busco_eukaryote_metaeuk -c tests/config/nextflow.config command: nextflow run tests/modules/busco -entry test_busco_eukaryote_metaeuk -c tests/config/nextflow.config
tags: tags:
- busco - busco
- eukaryote
- genome
- metaeuk
files: 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 - path: output/busco/versions.yml
md5sum: 34a808c257e6db1b0456f3b4372bc477 md5sum: 34a808c257e6db1b0456f3b4372bc477
@ -33,10 +104,9 @@
command: nextflow run tests/modules/busco -entry test_busco_eukaryote_augustus -c tests/config/nextflow.config command: nextflow run tests/modules/busco -entry test_busco_eukaryote_augustus -c tests/config/nextflow.config
tags: tags:
- busco - busco
- eukaryote
- genome
- augustus
files: files:
- path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
md5sum: 660393dd43cd6a093b952d4b8ad41e40
- path: output/busco/versions.yml - path: output/busco/versions.yml
md5sum: 2caac915461410b16a1524ac064cd0df md5sum: 2caac915461410b16a1524ac064cd0df
@ -44,9 +114,23 @@
command: nextflow run tests/modules/busco -entry test_busco_protein -c tests/config/nextflow.config command: nextflow run tests/modules/busco -entry test_busco_protein -c tests/config/nextflow.config
tags: tags:
- busco - busco
- bacteria
- proteins
files: 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 - path: output/busco/versions.yml
md5sum: d7392261a57960a7e6aea609dce824f5 md5sum: d7392261a57960a7e6aea609dce824f5
@ -54,8 +138,22 @@
command: nextflow run tests/modules/busco -entry test_busco_transcriptome -c tests/config/nextflow.config command: nextflow run tests/modules/busco -entry test_busco_transcriptome -c tests/config/nextflow.config
tags: tags:
- busco - busco
- bacteria
- transcriptome
files: 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 - path: output/busco/versions.yml
md5sum: 30eacbc7df70f6b1e72e0a7b6d02a7e1 md5sum: 30eacbc7df70f6b1e72e0a7b6d02a7e1