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Update BUSCO
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@dialvarezs
dialvarezs committed Dec 11, 2024
1 parent 4912a73 commit 5674aad
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Showing 5 changed files with 118 additions and 94 deletions.
3 changes: 2 additions & 1 deletion modules/nf-core/busco/busco/environment.yml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::busco=5.7.1
- bioconda::busco=5.8.2
10 changes: 6 additions & 4 deletions modules/nf-core/busco/busco/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process BUSCO_BUSCO {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/busco:5.7.1--pyhdfd78af_0':
'biocontainers/busco:5.7.1--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/busco:5.8.2--pyhdfd78af_0':
'biocontainers/busco:5.8.2--pyhdfd78af_0' }"

input:
tuple val(meta), path(fasta, stageAs:'tmp_input/*')
Expand Down Expand Up @@ -35,8 +35,10 @@ process BUSCO_BUSCO {
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
def busco_config = config_file ? "--config $config_file" : ''
def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}"
def busco_config = config_file ? "--config ${config_file}" : ''
def busco_lineage = lineage in [ 'auto', 'auto_prok', 'auto_euk']
? lineage.replaceFirst('auto', '--auto-lineage').replaceAll('_', '-')
: "--lineage_dataset ${lineage}"
def busco_lineage_dir = busco_lineages_path ? "--download_path ${busco_lineages_path}" : ''
"""
# Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
Expand Down
12 changes: 6 additions & 6 deletions modules/nf-core/busco/busco/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
]
input[1] = 'genome'
input[2] = 'bacteria_odb10' // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
input[2] = 'bacteria_odb12' // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
input[3] = [] // Download busco lineage
input[4] = [] // No config
"""
Expand Down Expand Up @@ -85,7 +85,7 @@ nextflow_process {
]
]
input[1] = 'genome'
input[2] = 'bacteria_odb10'
input[2] = 'bacteria_odb12'
input[3] = []
input[4] = []
"""
Expand Down Expand Up @@ -274,7 +274,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true)
]
input[1] = 'proteins'
input[2] = 'bacteria_odb10'
input[2] = 'bacteria_odb12'
input[3] = []
input[4] = []
"""
Expand Down Expand Up @@ -336,7 +336,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
]
input[1] = 'transcriptome'
input[2] = 'bacteria_odb10'
input[2] = 'bacteria_odb12'
input[3] = []
input[4] = []
"""
Expand Down Expand Up @@ -397,7 +397,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
]
input[1] = 'genome'
input[2] = 'bacteria_odb10'
input[2] = 'bacteria_odb12'
input[3] = []
input[4] = []
"""
Expand All @@ -412,4 +412,4 @@ nextflow_process {
}
}

}
}
161 changes: 91 additions & 70 deletions modules/nf-core/busco/busco/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
{
"id": "test"
},
"test-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
"test-bacteria_odb12-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
Expand Down Expand Up @@ -55,14 +55,14 @@
]
],
"9": [
"versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
"versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
],
"batch_summary": [
[
{
"id": "test"
},
"test-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
"test-bacteria_odb12-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"busco_dir": [
Expand Down Expand Up @@ -110,121 +110,142 @@

],
"versions": [
"versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
"versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
]
}
],
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"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
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"timestamp": "2024-12-11T12:45:52.045550047"
},
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"test_busco_genome_multi_fasta": {
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"timestamp": "2024-12-11T12:44:24.836011052"
},
"test_busco_eukaryote_metaeuk": {
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"timestamp": "2024-05-03T13:25:38.159041"
"timestamp": "2024-12-11T13:07:17.335085326"
},
"test_busco_transcriptome": {
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26 changes: 13 additions & 13 deletions subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,9 +46,9 @@

],
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],
"2": [

Expand Down Expand Up @@ -172,17 +172,17 @@

],
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"timestamp": "2024-12-11T12:47:54.913113837"
},
"candidatus_portiera_aleyrodidarum - bacteroides_fragilis - genome": {
"content": [
Expand All @@ -201,7 +201,7 @@
"mode": "genome",
"lineage": "bacteria_odb10"
},
"test-bacteria_odb10-busco.batch_summary.txt:md5,a1186bc25448ac1949bf7790810f7161"
"test-bacteria_odb10-busco.batch_summary.txt:md5,30d9e8403e21e0ac7fa9574a4a7ca825"
],
[
{
Expand Down Expand Up @@ -235,21 +235,21 @@
"mode": "proteins",
"lineage": "bacteria_odb10"
},
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"timestamp": "2024-05-13T16:39:04.376704"
"timestamp": "2024-12-11T12:47:41.989229128"
}
}

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