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Update to topics getorganelle/* #11561

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21 changes: 5 additions & 16 deletions modules/nf-core/getorganelle/config/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,16 +3,16 @@ process GETORGANELLE_CONFIG {
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/getorganelle:1.7.7.0--pyh7cba7a3_0':
'quay.io/biocontainers/getorganelle:1.7.7.0--pyh7cba7a3_0' }"
container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/getorganelle:1.7.7.0--pyh7cba7a3_0'
: 'quay.io/biocontainers/getorganelle:1.7.7.0--pyh7cba7a3_0'}"

input:
val(organelle_type)

output:
tuple val(organelle_type), path("getorganelle"), emit: db
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('getorganelle'), eval("get_organelle_config.py --version |& sed 's/^GetOrganelle v//'"), topic: versions, emit: versions_getorganelle

when:
task.ext.when == null || task.ext.when
Expand All @@ -21,25 +21,14 @@ process GETORGANELLE_CONFIG {
def args = task.ext.args ?: ''
"""
get_organelle_config.py \\
$args \\
${args} \\
-a ${organelle_type} \\
--config-dir getorganelle

cat <<-END_VERSIONS > versions.yml
"${task.process}":
getorganelle: \$(get_organelle_config.py --version | sed 's/^GetOrganelle v//g')
END_VERSIONS
"""

stub:

"""
mkdir -p getorganelle/{LabelDatabase,SeedDatabase}
touch getorganelle/{LabelDatabase,SeedDatabase}/${organelle_type}.fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
getorganelle: \$(get_organelle_config.py --version | sed 's/^GetOrganelle v//g')
END_VERSIONS
"""
}
30 changes: 22 additions & 8 deletions modules/nf-core/getorganelle/config/meta.yml
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Expand Up @@ -13,9 +13,9 @@ tools:
documentation: "https://github.com/Kinggerm/GetOrganelle"
tool_dev_url: "https://github.com/Kinggerm/GetOrganelle"
doi: "10.1186/s13059-020-02154-5"
licence: ["GPL v3"]
licence:
- "GPL v3"
identifier: biotools:getorganelle

input:
- organelle_type:
type: string
Expand All @@ -30,12 +30,26 @@ output:
- getorganelle:
type: directory
description: Downloaded database for GetOrganelle
versions_getorganelle:
- - ${task.process}:
type: string
description: The name of the process
- getorganelle:
type: string
description: Downloaded database for GetOrganelle
- get_organelle_config.py --version |& sed 's/^GetOrganelle v//':
type: eval
description: The expression to obtain the version of the tool
topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The name of the process
- getorganelle:
type: string
description: Downloaded database for GetOrganelle
- get_organelle_config.py --version |& sed 's/^GetOrganelle v//':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@erinyoung"
36 changes: 11 additions & 25 deletions modules/nf-core/getorganelle/config/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -15,36 +15,23 @@ nextflow_process {
process {
"""
input[0] = 'all'

"""
}
}

then {
assertAll(
{ assert process.success },
{
def all_files = []

file(process.out.db[0][1]).eachFileRecurse (FileType.FILES) { file ->
all_files << file
}

def all_file_names = all_files.collect { it.name }.toSorted()

def stable_file_names = [
'VERSION',
'animal_mt.fasta'
]

def stable_files = all_files.findAll { it.name in stable_file_names }.toSorted()

assert snapshot(
all_file_names,
stable_files,
process.out.versions[0]
).match()
}
{
def stable_name = getAllFilesFromDir(process.out.db[0][1].toString(), include:['*', '**/*'])
def stable_content = getAllFilesFromDir(process.out.db[0][1].toString(), include:["**/VERSION", "**/animal_mt.fasta"])

assert snapshot(
stable_name*.name.sort(),
stable_content,
process.out.findAll { key, val -> key.startsWith('versions') }
).match()
}
Comment on lines +25 to +34
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@SPPearce SPPearce May 7, 2026

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This has lost its indentation

)
}
}
Expand All @@ -55,15 +42,14 @@ nextflow_process {
process {
"""
input[0] = 'all'

"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
48 changes: 22 additions & 26 deletions modules/nf-core/getorganelle/config/tests/main.nf.test.snap
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Expand Up @@ -2,7 +2,7 @@
"test-getorganelle-config-stub": {
"content": [
{
"0": [
"db": [
[
"all",
[
Expand All @@ -15,32 +15,20 @@
]
]
],
"1": [
"versions.yml:md5,4e972ee1ef3a8d3509c9442fe644258b"
],
"db": [
"versions_getorganelle": [
[
"all",
[
[
"all.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
],
[
"all.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
"GETORGANELLE_CONFIG",
"getorganelle",
"1.7.7.0"
]
],
"versions": [
"versions.yml:md5,4e972ee1ef3a8d3509c9442fe644258b"
]
}
],
"timestamp": "2026-05-07T13:18:22.471441535",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-02T12:42:17.160676"
"nf-test": "0.9.5",
"nextflow": "25.10.4"
}
},
"test-getorganelle-config": {
"content": [
Expand Down Expand Up @@ -166,12 +154,20 @@
"VERSION:md5,f3d5d8493c18ca2e553a6012d1505310",
"animal_mt.fasta:md5,2833e57f91c231bd19d678d869ed05df"
],
"versions.yml:md5,4e972ee1ef3a8d3509c9442fe644258b"
{
"versions_getorganelle": [
[
"GETORGANELLE_CONFIG",
"getorganelle",
"1.7.7.0"
]
]
}
],
"timestamp": "2026-05-07T13:49:20.038930564",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-02T13:02:45.095312"
"nf-test": "0.9.5",
"nextflow": "25.10.4"
}
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/getorganelle/fromreads/environment.yml
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Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::getorganelle=1.7.7.1
- bioconda::getorganelle=1.7.7.0
5 changes: 2 additions & 3 deletions modules/nf-core/getorganelle/fromreads/main.nf
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Expand Up @@ -14,8 +14,7 @@ process GETORGANELLE_FROMREADS {
output:
tuple val(meta), path("results/${prefix}.${organelle_type}.fasta.gz"), emit: fasta, optional: true
path "results/*", emit: etc
// the rest of the result files
tuple val("${task.process}"), val('getorganelle_from_reads'), eval("get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p'"), topic: versions, emit: versions_getorganelle
tuple val("${task.process}"), val('getorganelle_from_reads'), eval("get_organelle_from_reads.py --version |& sed 's/^GetOrganelle //'"), topic: versions, emit: versions_getorganelle

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -49,6 +48,6 @@ process GETORGANELLE_FROMREADS {
mkdir results
touch results/test_1.fastq
touch results/test_2.fastq
echo ''| gzip > results/${prefix}.${organelle_type}.fasta.gz
echo "" | gzip > results/${prefix}.${organelle_type}.fasta.gz
"""
}
8 changes: 4 additions & 4 deletions modules/nf-core/getorganelle/fromreads/meta.yml
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Expand Up @@ -12,9 +12,9 @@ tools:
documentation: "https://github.com/Kinggerm/GetOrganelle"
tool_dev_url: "https://github.com/Kinggerm/GetOrganelle"
doi: "10.1186/s13059-020-02154-5"
licence: ["GPL v3"]
licence:
- "GPL v3"
identifier: biotools:getorganelle

input:
- - meta:
type: map
Expand Down Expand Up @@ -58,7 +58,7 @@ output:
- getorganelle_from_reads:
type: string
description: The name of the tool
- "get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p'":
- get_organelle_from_reads.py --version |& sed 's/^GetOrganelle //':
type: eval
description: The expression to obtain the version of the tool
topics:
Expand All @@ -69,7 +69,7 @@ topics:
- getorganelle_from_reads:
type: string
description: The name of the tool
- "get_organelle_from_reads.py --version 2>&1 | sed -n 's/GetOrganelle //p'":
- get_organelle_from_reads.py --version |& sed 's/^GetOrganelle //':
type: eval
description: The expression to obtain the version of the tool
authors:
Expand Down
20 changes: 5 additions & 15 deletions modules/nf-core/getorganelle/fromreads/tests/main.nf.test
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Expand Up @@ -25,14 +25,13 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
[
file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true)
]
]
input[1] = GETORGANELLE_CONFIG.out.db

"""
}
}
Expand All @@ -45,7 +44,8 @@ nextflow_process {
process.out.etc[0][1],
process.out.etc.flatten().collect { file(it).name }.sort(),
process.out.fasta,
process.out.findAll { key, val -> key.startsWith('versions') }).match('main_output') },
process.out.findAll { key, val -> key.startsWith('versions') }
).match() },
)
}

Expand All @@ -57,7 +57,7 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
[
file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true)
Expand All @@ -67,25 +67,15 @@ nextflow_process {
'animal_mt',
file('mock/getorganelle')
]

"""
}
}

then {
def fileList_results = process.out.etc.flatten().collect { file(it).name }.sort()
def fileList_fasta = file(process.out.fasta[0][1]).name
assertAll(
{ assert process.success },
{ assert snapshot(
fileList_results,
fileList_fasta,
process.out.findAll { key, val -> key.startsWith('versions') }
).match('file_list') }

{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

}

}
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