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mcstaging/phenoimager2mc topic versions (nf-core#10960)
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Lines changed: 104 additions & 45 deletions

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‎modules/nf-core/mcstaging/phenoimager2mc/main.nf‎

Lines changed: 2 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ process MCSTAGING_PHENOIMAGER2MC {
99

1010
output:
1111
tuple val(meta), path("*.tif"), emit: tif
12-
path "versions.yml" , emit: versions
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tuple val("${task.process}"), val('phenoimager2mc'), eval('python /phenoimager2mc/scripts/phenoimager2mc.py --version | sed "s/v//g"'), emit: versions_phenoimager2mc, topic: versions
1313

1414
when:
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task.ext.when == null || task.ext.when
@@ -29,10 +29,7 @@ process MCSTAGING_PHENOIMAGER2MC {
2929
-o "${prefix}.tif" \
3030
$args
3131
32-
cat <<-END_VERSIONS > versions.yml
33-
"${task.process}":
34-
phenoimager2mc: \$(python /phenoimager2mc/scripts/phenoimager2mc.py --version | sed 's/v//g')
35-
END_VERSIONS
32+
sed -i -E 's/UUID="urn:uuid:[[:xdigit:]]{8}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{12}"/ /g' ${prefix}.tif
3633
"""
3734

3835
stub:
@@ -44,9 +41,5 @@ process MCSTAGING_PHENOIMAGER2MC {
4441
"""
4542
touch input
4643
touch "${prefix}.tif"
47-
cat <<-END_VERSIONS > versions.yml
48-
"${task.process}":
49-
phenoimager2mc: \$(python /phenoimager2mc/scripts/phenoimager2mc.py --version | sed 's/v//g')
50-
END_VERSIONS
5144
"""
5245
}

‎modules/nf-core/mcstaging/phenoimager2mc/meta.yml‎

Lines changed: 28 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,6 @@
1-
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
21
name: "mcstaging_phenoimager2mc"
3-
description: Staging module for MCMICRO transforming PhenoImager .tif files into stacked
4-
and normalized ome-tif files per cycle, compatible as ASHLAR input.
2+
description: Staging module for MCMICRO transforming PhenoImager .tif files into
3+
stacked and normalized ome-tif files per cycle, compatible as ASHLAR input.
54
keywords:
65
- imaging
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- registration
@@ -14,9 +13,9 @@ tools:
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homepage: "https://github.com/SchapiroLabor/phenoimager2mc"
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documentation: "https://github.com/SchapiroLabor/phenoimager2mc/README.md"
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tool_dev_url: "https://github.com/SchapiroLabor/phenoimager2mc"
17-
licence: ["GPL-2.0 license"]
16+
licence:
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- "GPL-2.0 license"
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identifier: ""
19-
2019
input:
2120
- - meta:
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type: map
@@ -27,7 +26,6 @@ input:
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type: list
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description: Folder or list with .tif files of one cycle from PhenoImager
2928
output:
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#Only when we have meta
3129
tif:
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- - meta:
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type: map
@@ -36,16 +34,32 @@ output:
3634
e.g. `[ id:'sample1' ]`
3735
- "*.tif":
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type: file
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description: One output .tif file containing concatenated tiles of the cycle.
37+
description: One output .tif file containing concatenated tiles of the
38+
cycle.
4039
pattern: "*.{tif,tiff}"
41-
ontologies: []
40+
ontologies:
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- edam: http://edamontology.org/format_3591 # TIFF
42+
versions_phenoimager2mc:
43+
- - ${task.process}:
44+
type: string
45+
description: The name of the process
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- phenoimager2mc:
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type: string
48+
description: The name of the tool
49+
- python /phenoimager2mc/scripts/phenoimager2mc.py --version | sed "s/v//g":
50+
type: eval
51+
description: The expression to obtain the version of the tool
52+
topics:
4253
versions:
43-
- versions.yml:
44-
type: file
45-
description: File containing software versions
46-
pattern: "versions.yml"
47-
ontologies:
48-
- edam: http://edamontology.org/format_3750 # YAML
54+
- - ${task.process}:
55+
type: string
56+
description: The name of the process
57+
- phenoimager2mc:
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type: string
59+
description: The name of the tool
60+
- python /phenoimager2mc/scripts/phenoimager2mc.py --version | sed "s/v//g":
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type: eval
62+
description: The expression to obtain the version of the tool
4963
authors:
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- "@chiarasch"
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maintainers:

‎modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test‎

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -35,9 +35,7 @@ nextflow_process {
3535
then {
3636
assertAll (
3737
{ assert process.success },
38-
{ assert snapshot(
39-
file(process.out.tif[0][1]).name,
40-
process.out.versions).match() }
38+
{ assert snapshot(process.out).match() }
4139
)
4240
}
4341
}
@@ -70,9 +68,7 @@ test("phenoimager2mc - tif - stub") {
7068
then {
7169
assertAll (
7270
{ assert process.success },
73-
{ assert snapshot(
74-
file(process.out.tif[0][1]).name,
75-
process.out.versions).match() }
71+
{ assert snapshot(process.out).match() }
7672
)
7773
}
7874
}

‎modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test.snap‎

Lines changed: 72 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -1,28 +1,84 @@
11
{
22
"phenoimager2mc - tif - stub": {
33
"content": [
4-
"test.tif",
5-
[
6-
"versions.yml:md5,30d4a7af53d372a0700d388471500532"
7-
]
4+
{
5+
"0": [
6+
[
7+
{
8+
"id": "test"
9+
},
10+
"test.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
11+
]
12+
],
13+
"1": [
14+
[
15+
"MCSTAGING_PHENOIMAGER2MC",
16+
"phenoimager2mc",
17+
"0.2.2"
18+
]
19+
],
20+
"tif": [
21+
[
22+
{
23+
"id": "test"
24+
},
25+
"test.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
26+
]
27+
],
28+
"versions_phenoimager2mc": [
29+
[
30+
"MCSTAGING_PHENOIMAGER2MC",
31+
"phenoimager2mc",
32+
"0.2.2"
33+
]
34+
]
35+
}
836
],
37+
"timestamp": "2026-03-18T18:36:07.934385032",
938
"meta": {
10-
"nf-test": "0.9.0",
11-
"nextflow": "24.04.4"
12-
},
13-
"timestamp": "2024-09-02T13:32:48.124044814"
39+
"nf-test": "0.9.4",
40+
"nextflow": "25.10.4"
41+
}
1442
},
1543
"phenoimager2mc - tif": {
1644
"content": [
17-
"test.tif",
18-
[
19-
"versions.yml:md5,30d4a7af53d372a0700d388471500532"
20-
]
45+
{
46+
"0": [
47+
[
48+
{
49+
"id": "test"
50+
},
51+
"test.tif:md5,08027876fe05a9bb06ce76b063a7fade"
52+
]
53+
],
54+
"1": [
55+
[
56+
"MCSTAGING_PHENOIMAGER2MC",
57+
"phenoimager2mc",
58+
"0.2.2"
59+
]
60+
],
61+
"tif": [
62+
[
63+
{
64+
"id": "test"
65+
},
66+
"test.tif:md5,08027876fe05a9bb06ce76b063a7fade"
67+
]
68+
],
69+
"versions_phenoimager2mc": [
70+
[
71+
"MCSTAGING_PHENOIMAGER2MC",
72+
"phenoimager2mc",
73+
"0.2.2"
74+
]
75+
]
76+
}
2177
],
78+
"timestamp": "2026-03-18T18:35:59.662472365",
2279
"meta": {
23-
"nf-test": "0.9.0",
24-
"nextflow": "24.04.4"
25-
},
26-
"timestamp": "2024-09-02T13:17:56.890612618"
80+
"nf-test": "0.9.4",
81+
"nextflow": "25.10.4"
82+
}
2783
}
2884
}

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