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Update busco to v5.4.3 and tar small files (nf-core#1970)
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* Update busco to v5.4.3 and tar small files

* Fix file contain strings

* Swap md5sums to contains for variable files
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@mahesh-panchal @matthdsm
mahesh-panchal authored and matthdsm committed Aug 30, 2022
1 parent 2f24e85 commit 6f131aa
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Showing 4 changed files with 571 additions and 132 deletions.
6 changes: 3 additions & 3 deletions modules/busco/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BUSCO {
tag "$meta.id"
label 'process_medium'

conda (params.enable_conda ? "bioconda::busco=5.3.2" : null)
conda (params.enable_conda ? "bioconda::busco=5.4.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/busco:5.3.2--pyhdfd78af_0':
'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0':
'quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0' }"

input:
tuple val(meta), path('tmp_input/*')
Expand Down
90 changes: 6 additions & 84 deletions tests/modules/busco/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ workflow test_busco_genome_single_fasta {
input,
['bacteria_odb10', 'bacteroidetes_odb10'], // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
[], // Download busco lineage
[], // No config
[] // No config
)

/* Output tree:
Expand Down Expand Up @@ -63,84 +63,6 @@ workflow test_busco_genome_single_fasta {
│ └── busco.log
├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/test-bacteroidetes_odb10-busco.batch_summary.txt
└── versions.yml -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/versions.yml
Former Output tree -w 'auto':
/tmp/tmp846crjv2/busco/
├── short_summary.generic.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.json
├── short_summary.generic.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.txt
├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.json
├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.txt
├── short_summary.specific.bacteroidales_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.json
├── short_summary.specific.bacteroidales_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.txt
├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.json
├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
├── test-auto-busco -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/
│ ├── genome.fna/
│ │ ├── auto_lineage/
│ │ │ ├── run_archaea_odb10/
│ │ │ ├── run_bacteria_odb10/
│ │ │ └── run_eukaryota_odb10/
│ │ ├── logs/
│ │ │ ├── hmmsearch_err.log
│ │ │ ├── hmmsearch_out.log
│ │ │ ├── metaeuk_err.log
│ │ │ ├── metaeuk_out.log
│ │ │ ├── prodigal_err.log
│ │ │ ├── prodigal_out.log
│ │ │ ├── sepp_err.log
│ │ │ └── sepp_out.log
│ │ ├── prodigal_output/
│ │ │ └── predicted_genes/
│ │ ├── run_bacteria_odb10 -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/genome.fna/auto_lineage/run_bacteria_odb10/ [recursive, not followed]
│ │ └── run_bacteroidales_odb10/
│ │ ├── busco_sequences/
│ │ ├── full_table.tsv
│ │ ├── hmmer_output/
│ │ ├── missing_busco_list.tsv
│ │ ├── short_summary.json
│ │ └── short_summary.txt
│ └── logs/
│ └── busco.log
├── test-auto-busco.batch_summary.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco.batch_summary.txt
├── test-bacteria_odb10-busco -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco/
│ ├── genome.fna/
│ │ ├── logs/
│ │ │ ├── hmmsearch_err.log
│ │ │ ├── hmmsearch_out.log
│ │ │ ├── prodigal_err.log
│ │ │ └── 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
│ └── logs/
│ └── busco.log
├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco.batch_summary.txt
├── test-bacteroidetes_odb10-busco -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco/
│ ├── genome.fna/
│ │ ├── logs/
│ │ │ ├── hmmsearch_err.log
│ │ │ ├── hmmsearch_out.log
│ │ │ ├── prodigal_err.log
│ │ │ └── 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
│ └── logs/
│ └── busco.log
├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco.batch_summary.txt
└── versions.yml -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/versions.yml
*/

}
Expand All @@ -159,7 +81,7 @@ workflow test_busco_genome_multi_fasta {
input,
'bacteria_odb10',
[], // Download busco lineage
[], // No config
[] // No config
)

/* Output tree:
Expand Down Expand Up @@ -218,7 +140,7 @@ workflow test_busco_eukaryote_metaeuk {
input,
'eukaryota_odb10',
[], // Download busco lineage
[], // No config
[] // No config
)

/* Output tree:
Expand Down Expand Up @@ -259,7 +181,7 @@ workflow test_busco_eukaryote_augustus {
input,
'eukaryota_odb10',
[], // Download busco lineage
[], // No config
[] // No config
)

/* Output tree:
Expand Down Expand Up @@ -303,7 +225,7 @@ workflow test_busco_protein {
input,
'bacteria_odb10',
[], // Download busco lineage
[], // No config
[] // No config
)

/* Output tree:
Expand Down Expand Up @@ -339,7 +261,7 @@ workflow test_busco_transcriptome {
input,
'bacteria_odb10',
[], // Download busco lineage
[], // No config
[] // No config
)

/* Output tree:
Expand Down
12 changes: 6 additions & 6 deletions tests/modules/busco/nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -3,26 +3,26 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

withName: 'test_busco_genome_single_fasta:BUSCO' {
ext.args = '--mode genome'
ext.args = '--mode genome --tar'
}

withName: 'test_busco_genome_multi_fasta:BUSCO' {
ext.args = '--mode genome'
ext.args = '--mode genome --tar'
}

withName: 'test_busco_eukaryote_metaeuk:BUSCO' {
ext.args = '--mode genome'
ext.args = '--mode genome --tar'
}

withName: 'test_busco_eukaryote_augustus:BUSCO' {
ext.args = '--mode genome --augustus'
ext.args = '--mode genome --augustus --tar'
}

withName: 'test_busco_protein:BUSCO' {
ext.args = '--mode proteins'
ext.args = '--mode proteins --tar'
}

withName: 'test_busco_transcriptome:BUSCO'{
ext.args = '--mode transcriptome'
ext.args = '--mode transcriptome --tar'
}
}
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