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LouisLeNezetLouisLeNezet
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Update to topics homer/* (#11746)
* Update to topics * Update to topics * Update to topics * Update to topics * Update to topics * Update sbwf
1 parent c16f033 commit 9ed7f15

26 files changed

Lines changed: 622 additions & 558 deletions

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‎modules/nf-core/homer/annotatepeaks/main.nf‎

Lines changed: 2 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -14,16 +14,15 @@ process HOMER_ANNOTATEPEAKS {
1414
output:
1515
tuple val(meta), path("*annotatePeaks.txt"), emit: txt
1616
tuple val(meta), path("*annStats.txt"), emit: stats, optional: true
17-
path "versions.yml", emit: versions
17+
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
18+
tuple val("${task.process}"), val('homer'), val("4.11"), emit: versions_homer, topic: versions
1819

1920
when:
2021
task.ext.when == null || task.ext.when
2122

2223
script:
2324
def args = task.ext.args ?: ''
2425
def prefix = task.ext.prefix ?: "${meta.id}"
25-
def VERSION = '4.11'
26-
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
2726
"""
2827
annotatePeaks.pl \\
2928
${peak} \\
@@ -32,23 +31,11 @@ process HOMER_ANNOTATEPEAKS {
3231
-gtf ${gtf} \\
3332
-cpu ${task.cpus} \\
3433
> ${prefix}.annotatePeaks.txt
35-
36-
cat <<-END_VERSIONS > versions.yml
37-
"${task.process}":
38-
homer: ${VERSION}
39-
END_VERSIONS
4034
"""
4135

4236
stub:
4337
def prefix = task.ext.prefix ?: "${meta.id}"
44-
def VERSION = '4.11'
45-
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
4638
"""
4739
touch ${prefix}.annotatePeaks.txt
48-
49-
cat <<-END_VERSIONS > versions.yml
50-
"${task.process}":
51-
homer: ${VERSION}
52-
END_VERSIONS
5340
"""
5441
}

‎modules/nf-core/homer/annotatepeaks/meta.yml‎

Lines changed: 22 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,8 @@ tools:
1010
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
1111
documentation: http://homer.ucsd.edu/homer/
1212
doi: 10.1016/j.molcel.2010.05.004.
13-
licence: ["GPL-3.0-or-later"]
13+
licence:
14+
- "GPL-3.0-or-later"
1415
identifier: biotools:homer
1516
input:
1617
- - meta:
@@ -55,13 +56,27 @@ output:
5556
description: Annotation statistics in txt file
5657
pattern: "*annStats.txt"
5758
ontologies: []
59+
versions_homer:
60+
- - ${task.process}:
61+
type: string
62+
description: The name of the process
63+
- homer:
64+
type: string
65+
description: The name of the tool
66+
- "4.11":
67+
type: string
68+
description: The expression to obtain the version of the tool
69+
topics:
5870
versions:
59-
- versions.yml:
60-
type: file
61-
description: File containing software versions
62-
pattern: "versions.yml"
63-
ontologies:
64-
- edam: http://edamontology.org/format_3750 # YAML
71+
- - ${task.process}:
72+
type: string
73+
description: The name of the process
74+
- homer:
75+
type: string
76+
description: The name of the tool
77+
- "4.11":
78+
type: string
79+
description: The expression to obtain the version of the tool
6580
authors:
6681
- "@drpatelh"
6782
- "@kevinmenden"

‎modules/nf-core/homer/annotatepeaks/tests/main.nf.test‎

Lines changed: 2 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -30,12 +30,7 @@ nextflow_process {
3030
then {
3131
assertAll(
3232
{ assert process.success },
33-
{ assert snapshot(
34-
file(process.out.txt[0][1]).name, // unstable
35-
process.out.stats,
36-
process.out.versions
37-
).match()
38-
}
33+
{ assert snapshot(sanitizeOutput(process.out, unstableKeys:["txt"])).match()}
3934
)
4035
}
4136
}
@@ -60,7 +55,7 @@ nextflow_process {
6055
then {
6156
assertAll(
6257
{ assert process.success },
63-
{ assert snapshot(process.out).match("stub") }
58+
{ assert snapshot(sanitizeOutput(process.out)).match()}
6459
)
6560
}
6661
}

‎modules/nf-core/homer/annotatepeaks/tests/main.nf.test.snap‎

Lines changed: 37 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -1,42 +1,41 @@
11
{
22
"test-homer-annotatepeaks": {
3-
"content": [
4-
"test.annotatePeaks.txt",
5-
[
6-
[
7-
{
8-
"id": "test"
9-
},
10-
"test.annStats.txt:md5,eba336bce28fb5ec5d4ea3215b502dc5"
11-
]
12-
],
13-
[
14-
"versions.yml:md5,d109521b6e43672cf246fd269b3833c8"
15-
]
16-
],
17-
"meta": {
18-
"nf-test": "0.9.0",
19-
"nextflow": "24.04.4"
20-
},
21-
"timestamp": "2024-09-05T21:28:26.487711"
22-
},
23-
"stub": {
243
"content": [
254
{
26-
"0": [
5+
"stats": [
276
[
287
{
298
"id": "test"
309
},
31-
"test.annotatePeaks.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
10+
"test.annStats.txt:md5,eba336bce28fb5ec5d4ea3215b502dc5"
3211
]
3312
],
34-
"1": [
35-
36-
],
37-
"2": [
38-
"versions.yml:md5,d109521b6e43672cf246fd269b3833c8"
13+
"txt": [
14+
[
15+
{
16+
"id": "test"
17+
},
18+
"test.annotatePeaks.txt"
19+
]
3920
],
21+
"versions_homer": [
22+
[
23+
"HOMER_ANNOTATEPEAKS",
24+
"homer",
25+
"4.11"
26+
]
27+
]
28+
}
29+
],
30+
"timestamp": "2026-05-22T08:26:40.525503224",
31+
"meta": {
32+
"nf-test": "0.9.5",
33+
"nextflow": "26.04.0"
34+
}
35+
},
36+
"test-homer-annotatepeaks-stub": {
37+
"content": [
38+
{
4039
"stats": [
4140

4241
],
@@ -48,15 +47,19 @@
4847
"test.annotatePeaks.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
4948
]
5049
],
51-
"versions": [
52-
"versions.yml:md5,d109521b6e43672cf246fd269b3833c8"
50+
"versions_homer": [
51+
[
52+
"HOMER_ANNOTATEPEAKS",
53+
"homer",
54+
"4.11"
55+
]
5356
]
5457
}
5558
],
59+
"timestamp": "2026-05-22T08:26:51.670938012",
5660
"meta": {
57-
"nf-test": "0.9.2",
58-
"nextflow": "24.10.1"
59-
},
60-
"timestamp": "2024-11-23T14:37:35.102823"
61+
"nf-test": "0.9.5",
62+
"nextflow": "26.04.0"
63+
}
6164
}
6265
}

‎modules/nf-core/homer/findpeaks/main.nf‎

Lines changed: 2 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,8 @@ process HOMER_FINDPEAKS {
1212

1313
output:
1414
tuple val(meta), path("*.peaks.txt"), emit: txt
15-
path "versions.yml", emit: versions
15+
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
16+
tuple val("${task.process}"), val('homer'), val("4.11"), emit: versions_homer, topic: versions
1617

1718
when:
1819
task.ext.when == null || task.ext.when
@@ -21,33 +22,18 @@ process HOMER_FINDPEAKS {
2122
def args = task.ext.args ?: ''
2223
def prefix = task.ext.prefix ?: uniqmap ? "${meta.id}-${uniqmap.baseName}" : "${meta.id}"
2324
def uniqmap_flag = uniqmap ? "-uniqmap ${uniqmap}" : ""
24-
def VERSION = '4.11'
25-
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
2625
"""
2726
2827
findPeaks \\
2928
${tagDir} \\
3029
${args} \\
3130
-o ${prefix}.peaks.txt \\
3231
${uniqmap_flag}
33-
34-
cat <<-END_VERSIONS > versions.yml
35-
"${task.process}":
36-
homer: ${VERSION}
37-
END_VERSIONS
3832
"""
3933

4034
stub:
4135
def prefix = task.ext.prefix ?: "${meta.id}"
42-
def VERSION = '4.11'
43-
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
44-
4536
"""
4637
touch ${prefix}.peaks.txt
47-
48-
cat <<-END_VERSIONS > versions.yml
49-
"${task.process}":
50-
homer: ${VERSION}
51-
END_VERSIONS
5238
"""
5339
}

‎modules/nf-core/homer/findpeaks/meta.yml‎

Lines changed: 22 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,8 @@ tools:
1212
documentation: "http://homer.ucsd.edu/homer/"
1313
tool_dev_url: "http://homer.ucsd.edu/homer/ngs/peaks.html"
1414
doi: 10.1016/j.molcel.2010.05.004.
15-
licence: ["GPL-3.0-or-later"]
15+
licence:
16+
- "GPL-3.0-or-later"
1617
identifier: biotools:homer
1718
input:
1819
- - meta:
@@ -41,13 +42,27 @@ output:
4142
description: "Peaks in txt file"
4243
pattern: "*.peaks.txt"
4344
ontologies: []
45+
versions_homer:
46+
- - ${task.process}:
47+
type: string
48+
description: The name of the process
49+
- homer:
50+
type: string
51+
description: The name of the tool
52+
- "4.11":
53+
type: string
54+
description: The expression to obtain the version of the tool
55+
topics:
4456
versions:
45-
- versions.yml:
46-
type: file
47-
description: File containing software versions
48-
pattern: "versions.yml"
49-
ontologies:
50-
- edam: http://edamontology.org/format_3750 # YAML
57+
- - ${task.process}:
58+
type: string
59+
description: The name of the process
60+
- homer:
61+
type: string
62+
description: The name of the tool
63+
- "4.11":
64+
type: string
65+
description: The expression to obtain the version of the tool
5166
authors:
5267
- "@edmundmiller"
5368
maintainers:

‎modules/nf-core/homer/findpeaks/tests/main.nf.test‎

Lines changed: 3 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -58,7 +58,7 @@ nextflow_process {
5858
then {
5959
assertAll(
6060
{ assert process.success },
61-
{ assert snapshot(process.out).match("tagdir") }
61+
{ assert snapshot(sanitizeOutput(process.out)).match()}
6262
)
6363
}
6464

@@ -80,15 +80,12 @@ nextflow_process {
8080
then {
8181
assertAll(
8282
{ assert process.success },
83-
{ assert snapshot(process.out).match("stub") }
83+
{ assert snapshot(sanitizeOutput(process.out)).match()}
8484
)
8585
}
8686
}
8787

8888
test("sarscov2 - tagdir - uniqmap") {
89-
90-
tag "uniqmap"
91-
9289
when {
9390
process {
9491
"""
@@ -101,13 +98,7 @@ nextflow_process {
10198
then {
10299
assertAll(
103100
{ assert process.success },
104-
{ assert snapshot(
105-
process.out,
106-
// FIXME These are empty?
107-
path(process.out.txt.get(0).get(1)).readLines()[31],
108-
path(process.out.txt.get(0).get(1)).readLines()[33],
109-
).match()
110-
}
101+
{ assert snapshot(sanitizeOutput(process.out)).match()}
111102
)
112103
}
113104
}

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