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Merged
LouisLeNezet merged 1 commit into from
Jun 22, 2026
Merged

Update to topics mageck/* #12111

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28 changes: 9 additions & 19 deletions modules/nf-core/mageck/count/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,42 +12,32 @@ process MAGECK_COUNT {
path(library)

output:
tuple val(meta), path("*count.txt") , emit: count
tuple val(meta), path("*count.txt") , emit: count
tuple val(meta), path("*.count_normalized.txt"), emit: norm
path "versions.yml" , emit: versions
tuple val("${task.process}"), val("mageck"), eval("mageck -v"), emit: versions_mageck, topic: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def input_file = ("$inputfile".endsWith(".fastq.gz")) ? "--fastq ${inputfile}" : "-k ${inputfile}"
def sample_label = ("$inputfile".endsWith(".fastq.gz") || "$inputfile".endsWith(".fq.gz")) ? "--sample-label ${meta.id}" : ''
def input_file = ("${inputfile}".endsWith(".fastq.gz")) ? "--fastq ${inputfile}" : "-k ${inputfile}"
def sample_label = ("${inputfile}".endsWith(".fastq.gz") || "${inputfile}".endsWith(".fq.gz")) ? "--sample-label ${meta.id}" : ''

"""
mageck \\
count \\
$args \\
-l $library \\
-n $prefix \\
$sample_label \\
$input_file \\


cat <<-END_VERSIONS > versions.yml
"${task.process}":
mageck: \$(mageck -v)
END_VERSIONS
${args} \\
-l ${library} \\
-n ${prefix} \\
${sample_label} \\
${input_file}
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.count.txt
touch ${prefix}.count_normalized.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
mageck: \$(mageck -v)
END_VERSIONS
"""
}
39 changes: 28 additions & 11 deletions modules/nf-core/mageck/count/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
name: "mageck_count"
description: mageck count for functional genomics, reads are usually mapped to a specific
sgRNA
description: mageck count for functional genomics, reads are usually mapped to a
specific sgRNA
keywords:
- sort
- functional genomics
Expand All @@ -13,7 +13,8 @@ tools:
homepage: "https://sourceforge.net/p/mageck/wiki/Home/"
documentation: "https://sourceforge.net/p/mageck/wiki/demo/#step-4-run-the-mageck-count-command"
doi: "10.1186/s13059-014-0554-4"
licence: ["BSD License"]
licence:
- "BSD License"
identifier: biotools:mageck
input:
- - meta:
Expand All @@ -23,8 +24,8 @@ input:
e.g. [ id:'test', single_end:false ]
- inputfile:
type: file
description: library fastq file containing the sgRNA and gene name or count
table containing the sgRNA and number of reads to per sample
description: library fastq file containing the sgRNA and gene name or
count table containing the sgRNA and number of reads to per sample
pattern: "*.{fq,fastq,fastq.gz,fq.gz,csv,txt,tsv}"
ontologies:
- edam: http://edamontology.org/format_1930 # FASTQ
Expand Down Expand Up @@ -60,13 +61,29 @@ output:
description: File containing normalized read counts
pattern: "*.count_normalized.txt"
ontologies: []
versions_mageck:
- - ${task.process}:
type: string
description: The name of the process
- mageck:
type: string
description: The name of the tool
- mageck -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
- mageck:
type: string
description: The name of the tool
- mageck -v:
type: eval
description: The expression to obtain the version of the tool

authors:
- "@LaurenceKuhl"
maintainers:
Expand Down
23 changes: 14 additions & 9 deletions modules/nf-core/mageck/count/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,12 @@ nextflow_process {
when {
process {
"""
input[0] = [ [ id:'test,test2', single_end:true] , // meta map
[file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376999.small.fastq.gz', checkIfExists: true)]
input[0] = [
[ id:'test,test2' ],
[
file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376999.small.fastq.gz', checkIfExists: true)
]
]
input[1] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/yusa_library.csv')
"""
Expand All @@ -26,7 +29,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand All @@ -39,9 +42,12 @@ nextflow_process {
when {
process {
"""
input[0] = [ [ id:'test,test2', single_end:true] , // meta map
[file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376999.small.fastq.gz', checkIfExists: true)]
input[0] = [
[ id:'test,test2' ],
[
file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376999.small.fastq.gz', checkIfExists: true)
]
]
input[1] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/yusa_library.csv')
"""
Expand All @@ -51,8 +57,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match()
}
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand Down
82 changes: 26 additions & 56 deletions modules/nf-core/mageck/count/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,99 +2,69 @@
"mus_musculus - fastq": {
"content": [
{
"0": [
[
{
"id": "test,test2",
"single_end": true
},
"test,test2.count.txt:md5,2759bdc010998f863518cf7a2df812dc"
]
],
"1": [
[
{
"id": "test,test2",
"single_end": true
},
"test,test2.count_normalized.txt:md5,d79f3863168ee0f0750a59d94f70ce1a"
]
],
"2": [
"versions.yml:md5,8fd54f61f3c77976003f79397f6b12d9"
],
"count": [
[
{
"id": "test,test2",
"single_end": true
"id": "test,test2"
},
"test,test2.count.txt:md5,2759bdc010998f863518cf7a2df812dc"
]
],
"norm": [
[
{
"id": "test,test2",
"single_end": true
"id": "test,test2"
},
"test,test2.count_normalized.txt:md5,d79f3863168ee0f0750a59d94f70ce1a"
]
],
"versions": [
"versions.yml:md5,8fd54f61f3c77976003f79397f6b12d9"
"versions_mageck": [
[
"MAGECK_COUNT",
"mageck",
"0.5.9.5"
]
]
}
],
"timestamp": "2024-06-14T17:31:00.990366"
"timestamp": "2026-06-19T14:46:05.983468802",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.3"
}
},
"mus_musculus - fastq - stub": {
"content": [
{
"0": [
[
{
"id": "test,test2",
"single_end": true
},
"test,test2.count.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test,test2",
"single_end": true
},
"test,test2.count_normalized.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
"versions.yml:md5,8fd54f61f3c77976003f79397f6b12d9"
],
"count": [
[
{
"id": "test,test2",
"single_end": true
"id": "test,test2"
},
"test,test2.count.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"norm": [
[
{
"id": "test,test2",
"single_end": true
"id": "test,test2"
},
"test,test2.count_normalized.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,8fd54f61f3c77976003f79397f6b12d9"
"versions_mageck": [
[
"MAGECK_COUNT",
"mageck",
"0.5.9.5"
]
]
}
],
"timestamp": "2024-06-14T17:31:12.173269"
"timestamp": "2026-06-19T14:46:14.042271757",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.3"
}
}
}
22 changes: 6 additions & 16 deletions modules/nf-core/mageck/mle/main.nf
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Expand Up @@ -14,7 +14,7 @@ process MAGECK_MLE {
output:
tuple val(meta), path("*.gene_summary.txt") , emit: gene_summary
tuple val(meta), path("*.sgrna_summary.txt"), emit: sgrna_summary
path "versions.yml" , emit: versions
tuple val("${task.process}"), val("mageck"), eval("mageck -v"), emit: versions_mageck, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -26,28 +26,18 @@ process MAGECK_MLE {
"""
mageck \\
mle \\
$args \\
--threads $task.cpus \\
-k $count_table \\
-d $design_matrix \\
-n $prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
mageck: \$(mageck -v)
END_VERSIONS
${args} \\
--threads ${task.cpus} \\
-k ${count_table} \\
-d ${design_matrix} \\
-n ${prefix}
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"

"""
touch ${prefix}.gene_summary.txt
touch ${prefix}.sgrna_summary.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
mageck: \$(mageck -v)
END_VERSIONS
"""


Expand Down
31 changes: 24 additions & 7 deletions modules/nf-core/mageck/mle/meta.yml
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Expand Up @@ -12,7 +12,8 @@ tools:
documentation: "https://sourceforge.net/p/mageck/wiki/Home/"
tool_dev_url: "https://bitbucket.org/liulab/mageck/src"
doi: "10.1186/s13059-015-0843-6"
licence: ["BSD"]
licence:
- "BSD"
identifier: biotools:mageck
input:
- - meta:
Expand Down Expand Up @@ -63,13 +64,29 @@ output:
associated gene
pattern: "*.{gene_summary}"
ontologies: []
versions_mageck:
- - ${task.process}:
type: string
description: The name of the process
- mageck:
type: string
description: The name of the tool
- mageck -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
- mageck:
type: string
description: The name of the tool
- mageck -v:
type: eval
description: The expression to obtain the version of the tool

authors:
- "@LaurenceKuhl"
maintainers:
Expand Down
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