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LouisLeNezetLouisLeNezet
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Update to topic maxquant (#12203)
Update to topic
1 parent 7abb093 commit 2e70494

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Lines changed: 78 additions & 94 deletions

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‎modules/nf-core/maxquant/lfq/main.nf‎

Lines changed: 1 addition & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@ process MAXQUANT_LFQ {
1212

1313
output:
1414
tuple val(meta), path("${prefix}/*.txt"), emit: maxquant_txt
15-
path "versions.yml" , emit: versions
15+
tuple val("${task.process}"), val("maxquant"), eval("maxquant --version 2>&1 | sed 's/MaxQuantCmd //' || true"), emit: versions_maxquant, topic: versions
1616

1717
when:
1818
task.ext.when == null || task.ext.when
@@ -29,11 +29,6 @@ process MAXQUANT_LFQ {
2929
${args} \\
3030
mqpar_changed.xml
3131
mv combined/txt/*.txt ${prefix}/
32-
33-
cat <<-END_VERSIONS > versions.yml
34-
"${task.process}":
35-
maxquant: \$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \")
36-
END_VERSIONS
3732
"""
3833

3934
stub:
@@ -54,10 +49,5 @@ process MAXQUANT_LFQ {
5449
touch ${prefix}/peptides.txt
5550
touch ${prefix}/proteinGroups.txt
5651
touch ${prefix}/summary.txt
57-
58-
cat <<-END_VERSIONS > versions.yml
59-
"${task.process}":
60-
maxquant: \$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \")
61-
END_VERSIONS
6252
"""
6353
}

‎modules/nf-core/maxquant/lfq/meta.yml‎

Lines changed: 29 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,19 @@
11
name: maxquant_lfq
2-
description: Run standard proteomics data analysis with MaxQuant, mostly dedicated
3-
to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER"
2+
description: Run standard proteomics data analysis with MaxQuant, mostly
3+
dedicated to label-free. Paths to fasta and raw files needs to be marked by
4+
"PLACEHOLDER"
45
keywords:
56
- sort
67
- proteomics
78
- mass-spectroscopy
89
tools:
910
- maxquant:
10-
description: MaxQuant is a quantitative proteomics software package designed for
11-
analyzing large mass-spectrometric data sets. License restricted.
11+
description: MaxQuant is a quantitative proteomics software package designed
12+
for analyzing large mass-spectrometric data sets. License restricted.
1213
homepage: https://www.maxquant.org/
1314
documentation: http://coxdocs.org/doku.php?id=maxquant:start
14-
licence: ["http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf"]
15+
licence:
16+
- "http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf"
1517
identifier: biotools:maxquant
1618
input:
1719
- - meta:
@@ -45,13 +47,29 @@ output:
4547
description: tables with peptides and protein information
4648
pattern: "*.{txt}"
4749
ontologies: []
50+
versions_maxquant:
51+
- - ${task.process}:
52+
type: string
53+
description: The name of the process
54+
- maxquant:
55+
type: string
56+
description: The name of the tool
57+
- maxquant --version 2>&1 | sed 's/MaxQuantCmd //' || true:
58+
type: eval
59+
description: The expression to obtain the version of the tool
60+
61+
topics:
4862
versions:
49-
- versions.yml:
50-
type: file
51-
description: File containing software version
52-
pattern: "versions.yml"
53-
ontologies:
54-
- edam: http://edamontology.org/format_3750 # YAML
63+
- - ${task.process}:
64+
type: string
65+
description: The name of the process
66+
- maxquant:
67+
type: string
68+
description: The name of the tool
69+
- maxquant --version 2>&1 | sed 's/MaxQuantCmd //' || true:
70+
type: eval
71+
description: The expression to obtain the version of the tool
72+
5573
authors:
5674
- "@veitveit"
5775
maintainers:

‎modules/nf-core/maxquant/lfq/tests/main.nf.test‎

Lines changed: 5 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ nextflow_process {
1919
file(params.modules_testdata_base_path + 'proteomics/database/yeast_UPS.fasta', checkIfExists:true),
2020
file(params.modules_testdata_base_path + 'proteomics/parameter/mqpar.xml', checkIfExists:true)
2121
]
22-
input[1] = Channel.of([
22+
input[1] = channel.of([
2323
file(params.modules_testdata_base_path + 'proteomics/msspectra/OVEMB150205_12.raw'),
2424
file(params.modules_testdata_base_path + 'proteomics/msspectra/OVEMB150205_14.raw')
2525
]).collect()
@@ -29,18 +29,13 @@ nextflow_process {
2929
then {
3030
assertAll(
3131
{ assert process.success },
32-
{ assert snapshot( // Need to check only the file names as empty files are created
33-
process.out.maxquant_txt.collect{
34-
it[1].collect{ file(it).getName() }
35-
},
36-
process.out.versions,
37-
).match() }
32+
// Need to check only the file names as empty files are created
33+
{ assert snapshot(sanitizeOutput(process.out, unstableKeys:["maxquant_txt"])).match() }
3834
)
3935
}
4036
}
4137

4238
test("yeast_UPS - msspectra raw -- stub") {
43-
tag "stub"
4439
options "-stub"
4540
when {
4641
process {
@@ -50,7 +45,7 @@ nextflow_process {
5045
file(params.modules_testdata_base_path + 'proteomics/database/yeast_UPS.fasta', checkIfExists:true),
5146
file(params.modules_testdata_base_path + 'proteomics/parameter/mqpar.xml', checkIfExists:true)
5247
]
53-
input[1] = Channel.of([
48+
input[1] = channel.of([
5449
file(params.modules_testdata_base_path + 'proteomics/msspectra/OVEMB150205_12.raw'),
5550
file(params.modules_testdata_base_path + 'proteomics/msspectra/OVEMB150205_14.raw')
5651
]).collect()
@@ -60,10 +55,7 @@ nextflow_process {
6055
then {
6156
assertAll(
6257
{ assert process.success },
63-
{ assert snapshot(
64-
process.out,
65-
path(process.out.versions[0]).yaml
66-
).match() }
58+
{ assert snapshot(sanitizeOutput(process.out)).match() }
6759
)
6860
}
6961
}

‎modules/nf-core/maxquant/lfq/tests/main.nf.test.snap‎

Lines changed: 43 additions & 59 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
"yeast_UPS - msspectra raw -- stub": {
33
"content": [
44
{
5-
"0": [
5+
"maxquant_txt": [
66
[
77
{
88
"id": "test"
@@ -25,76 +25,60 @@
2525
]
2626
]
2727
],
28-
"1": [
29-
"versions.yml:md5,60dc5d20588a3b49c7d0c453bd98c5ee"
30-
],
28+
"versions_maxquant": [
29+
[
30+
"MAXQUANT_LFQ",
31+
"maxquant",
32+
"2.0.3.0"
33+
]
34+
]
35+
}
36+
],
37+
"timestamp": "2026-06-30T15:43:06.639002941",
38+
"meta": {
39+
"nf-test": "0.9.5",
40+
"nextflow": "26.04.3"
41+
}
42+
},
43+
"yeast_UPS - msspectra raw": {
44+
"content": [
45+
{
3146
"maxquant_txt": [
3247
[
3348
{
3449
"id": "test"
3550
},
3651
[
37-
"Oxidation (M)Sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
38-
"allPeptides.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
39-
"evidence.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
40-
"matchedFeatures.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
41-
"modificationSpecificPeptides.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
42-
"ms3Scans.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
43-
"msScans.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
44-
"msms.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
45-
"msmsScans.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
46-
"mzRange.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
47-
"parameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
48-
"peptides.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
49-
"proteinGroups.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
50-
"summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
52+
"Oxidation (M)Sites.txt",
53+
"allPeptides.txt",
54+
"evidence.txt",
55+
"matchedFeatures.txt",
56+
"modificationSpecificPeptides.txt",
57+
"ms3Scans.txt",
58+
"msScans.txt",
59+
"msms.txt",
60+
"msmsScans.txt",
61+
"mzRange.txt",
62+
"parameters.txt",
63+
"peptides.txt",
64+
"proteinGroups.txt",
65+
"summary.txt"
5166
]
5267
]
5368
],
54-
"versions": [
55-
"versions.yml:md5,60dc5d20588a3b49c7d0c453bd98c5ee"
69+
"versions_maxquant": [
70+
[
71+
"MAXQUANT_LFQ",
72+
"maxquant",
73+
"2.0.3.0"
74+
]
5675
]
57-
},
58-
{
59-
"MAXQUANT_LFQ": {
60-
"maxquant": "2.0.3.0"
61-
}
6276
}
6377
],
78+
"timestamp": "2026-06-30T16:12:14.910445538",
6479
"meta": {
65-
"nf-test": "0.9.2",
66-
"nextflow": "24.10.4"
67-
},
68-
"timestamp": "2025-05-07T17:41:13.129192804"
69-
},
70-
"yeast_UPS - msspectra raw": {
71-
"content": [
72-
[
73-
[
74-
"Oxidation (M)Sites.txt",
75-
"allPeptides.txt",
76-
"evidence.txt",
77-
"matchedFeatures.txt",
78-
"modificationSpecificPeptides.txt",
79-
"ms3Scans.txt",
80-
"msScans.txt",
81-
"msms.txt",
82-
"msmsScans.txt",
83-
"mzRange.txt",
84-
"parameters.txt",
85-
"peptides.txt",
86-
"proteinGroups.txt",
87-
"summary.txt"
88-
]
89-
],
90-
[
91-
"versions.yml:md5,60dc5d20588a3b49c7d0c453bd98c5ee"
92-
]
93-
],
94-
"meta": {
95-
"nf-test": "0.9.2",
96-
"nextflow": "24.10.4"
97-
},
98-
"timestamp": "2025-05-07T17:40:29.652923118"
80+
"nf-test": "0.9.5",
81+
"nextflow": "26.04.3"
82+
}
9983
}
10084
}

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