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Bump shinyngs version and migrate to topic channels (#11210)
* Bump shinyngs version and migrate to topic channels * Fix linting error
1 parent 8e79eb4 commit f484e07

19 files changed

Lines changed: 274 additions & 174 deletions

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‎modules/nf-core/shinyngs/app/environment.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,4 +4,4 @@ channels:
44
- conda-forge
55
- bioconda
66
dependencies:
7-
- bioconda::r-shinyngs=2.3.0
7+
- bioconda::r-shinyngs=2.4.0

‎modules/nf-core/shinyngs/app/main.nf‎

Lines changed: 3 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -14,8 +14,8 @@ process SHINYNGS_APP {
1414

1515
conda "${moduleDir}/environment.yml"
1616
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
17-
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d0/d0937af0a2b5efe1c18565ef320956e630a03c00c6d75ea5df92ec9f9ff2d14e/data' :
18-
'community.wave.seqera.io/library/r-shinyngs:2.3.0--140cda6231347fbb' }"
17+
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d7/d782b4f11adf8f3cad6af74ea585468decd873a171da1dae0e4a24a82bb29020/data' :
18+
'community.wave.seqera.io/library/r-shinyngs:2.4.0--709fc6932be670a5' }"
1919

2020
input:
2121
tuple val(meta), path(sample), path(feature_meta), path(assay_files) // Experiment-level info
@@ -24,7 +24,7 @@ process SHINYNGS_APP {
2424

2525
output:
2626
tuple val(meta), path("*/data.rds"), path("*/app.R") , emit: app
27-
path "versions.yml" , emit: versions
27+
tuple val("${task.process}"), val('shinyngs'), eval('Rscript -e "library(shinyngs); cat(as.character(packageVersion(\'shinyngs\')))"'), emit: versions_shinyngs, topic: versions
2828

2929
when:
3030
task.ext.when == null || task.ext.when
@@ -45,11 +45,6 @@ process SHINYNGS_APP {
4545
--differential_results "${differential_results.join(',')}" \\
4646
--output_dir "$prefix" \\
4747
$args \\
48-
49-
cat <<-END_VERSIONS > versions.yml
50-
"${task.process}":
51-
r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
52-
END_VERSIONS
5348
"""
5449

5550
stub:
@@ -59,11 +54,6 @@ process SHINYNGS_APP {
5954
mkdir -p "$prefix"
6055
touch "${prefix}/data.rds"
6156
touch "${prefix}/app.R"
62-
63-
cat <<-END_VERSIONS > versions.yml
64-
"${task.process}":
65-
r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
66-
END_VERSIONS
6757
"""
6858

6959
}

‎modules/nf-core/shinyngs/app/meta.yml‎

Lines changed: 21 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -76,13 +76,28 @@ output:
7676
pattern: "app/app.R"
7777
ontologies:
7878
- edam: http://edamontology.org/format_3999 # R script
79+
versions_shinyngs:
80+
- - ${task.process}:
81+
type: string
82+
description: The name of the process
83+
- shinyngs:
84+
type: string
85+
description: The name of the tool
86+
- 'Rscript -e "library(shinyngs); cat(as.character(packageVersion(''shinyngs'')))"':
87+
type: eval
88+
description: The expression to obtain the version of the tool
89+
90+
topics:
7991
versions:
80-
- versions.yml:
81-
type: file
82-
description: File containing software versions
83-
pattern: "versions.yml"
84-
ontologies:
85-
- edam: http://edamontology.org/format_3750 # YAML
92+
- - ${task.process}:
93+
type: string
94+
description: The name of the process
95+
- shinyngs:
96+
type: string
97+
description: The name of the tool
98+
- 'Rscript -e "library(shinyngs); cat(as.character(packageVersion(''shinyngs'')))"':
99+
type: eval
100+
description: The expression to obtain the version of the tool
86101
authors:
87102
- "@pinin4fjords"
88103
maintainers:

‎modules/nf-core/shinyngs/app/tests/main.nf.test‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,7 @@ nextflow_process {
4848
{ assert snapshot(
4949
file(process.out.app[0][1]).name,
5050
process.out.app[0][2],
51-
process.out.versions
51+
process.out.findAll { key, val -> key.startsWith('versions') }
5252
).match() }
5353
)
5454
}
@@ -89,7 +89,7 @@ nextflow_process {
8989
{ assert snapshot(
9090
file(process.out.app[0][1]).name,
9191
process.out.app[0][2],
92-
process.out.versions
92+
process.out.findAll { key, val -> key.startsWith('versions') }
9393
).match() }
9494
)
9595
}
@@ -132,7 +132,7 @@ nextflow_process {
132132
{ assert snapshot(
133133
file(process.out.app[0][1]).name,
134134
process.out.app[0][2],
135-
process.out.versions
135+
process.out.findAll { key, val -> key.startsWith('versions') }
136136
).match() }
137137
)
138138
}

‎modules/nf-core/shinyngs/app/tests/main.nf.test.snap‎

Lines changed: 39 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -3,42 +3,60 @@
33
"content": [
44
"data.rds",
55
"app.R:md5,d41d8cd98f00b204e9800998ecf8427e",
6-
[
7-
"versions.yml:md5,01db56d3cdd2e134e65df5465ea4eb0c"
8-
]
6+
{
7+
"versions_shinyngs": [
8+
[
9+
"SHINYNGS_APP",
10+
"shinyngs",
11+
"2.4.0"
12+
]
13+
]
14+
}
915
],
16+
"timestamp": "2026-04-16T19:21:39.140663074",
1017
"meta": {
11-
"nf-test": "0.9.3",
12-
"nextflow": "25.10.0"
13-
},
14-
"timestamp": "2025-12-01T17:45:00.111194977"
18+
"nf-test": "0.9.4",
19+
"nextflow": "25.10.4"
20+
}
1521
},
1622
"mouse - multi matrix": {
1723
"content": [
1824
"data.rds",
1925
"app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
20-
[
21-
"versions.yml:md5,01db56d3cdd2e134e65df5465ea4eb0c"
22-
]
26+
{
27+
"versions_shinyngs": [
28+
[
29+
"SHINYNGS_APP",
30+
"shinyngs",
31+
"2.4.0"
32+
]
33+
]
34+
}
2335
],
36+
"timestamp": "2026-04-16T19:21:09.728388372",
2437
"meta": {
25-
"nf-test": "0.9.3",
26-
"nextflow": "25.10.0"
27-
},
28-
"timestamp": "2025-12-01T17:44:28.229851192"
38+
"nf-test": "0.9.4",
39+
"nextflow": "25.10.4"
40+
}
2941
},
3042
"mouse - single matrix": {
3143
"content": [
3244
"data.rds",
3345
"app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
34-
[
35-
"versions.yml:md5,01db56d3cdd2e134e65df5465ea4eb0c"
36-
]
46+
{
47+
"versions_shinyngs": [
48+
[
49+
"SHINYNGS_APP",
50+
"shinyngs",
51+
"2.4.0"
52+
]
53+
]
54+
}
3755
],
56+
"timestamp": "2026-04-16T19:21:26.989003371",
3857
"meta": {
39-
"nf-test": "0.9.3",
40-
"nextflow": "25.10.0"
41-
},
42-
"timestamp": "2025-12-01T17:44:47.274942197"
58+
"nf-test": "0.9.4",
59+
"nextflow": "25.10.4"
60+
}
4361
}
4462
}

‎modules/nf-core/shinyngs/staticdifferential/environment.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,4 +4,4 @@ channels:
44
- conda-forge
55
- bioconda
66
dependencies:
7-
- bioconda::r-shinyngs=2.3.0
7+
- bioconda::r-shinyngs=2.4.0

‎modules/nf-core/shinyngs/staticdifferential/main.nf‎

Lines changed: 3 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@ process SHINYNGS_STATICDIFFERENTIAL {
44

55
conda "${moduleDir}/environment.yml"
66
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d0/d0937af0a2b5efe1c18565ef320956e630a03c00c6d75ea5df92ec9f9ff2d14e/data' :
8-
'community.wave.seqera.io/library/r-shinyngs:2.3.0--140cda6231347fbb' }"
7+
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d7/d782b4f11adf8f3cad6af74ea585468decd873a171da1dae0e4a24a82bb29020/data' :
8+
'community.wave.seqera.io/library/r-shinyngs:2.4.0--709fc6932be670a5' }"
99

1010
input:
1111
tuple val(meta), path(differential_result) // Differential info: contrast and differential stats
@@ -14,7 +14,7 @@ process SHINYNGS_STATICDIFFERENTIAL {
1414
output:
1515
tuple val(meta), path("*/png/volcano.png") , emit: volcanos_png
1616
tuple val(meta), path("*/html/volcano.html") , emit: volcanos_html, optional: true
17-
path "versions.yml" , emit: versions
17+
tuple val("${task.process}"), val('shinyngs'), eval('Rscript -e "library(shinyngs); cat(as.character(packageVersion(\'shinyngs\')))"'), emit: versions_shinyngs, topic: versions
1818

1919
when:
2020
task.ext.when == null || task.ext.when
@@ -30,11 +30,6 @@ process SHINYNGS_STATICDIFFERENTIAL {
3030
--feature_metadata "$feature_meta" \\
3131
--outdir "$prefix" \\
3232
$args
33-
34-
cat <<-END_VERSIONS > versions.yml
35-
"${task.process}":
36-
r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
37-
END_VERSIONS
3833
"""
3934

4035
stub:
@@ -43,10 +38,5 @@ process SHINYNGS_STATICDIFFERENTIAL {
4338
mkdir -p $prefix/png && mkdir $prefix/html
4439
touch $prefix/png/volcano.png
4540
touch $prefix/html/volcano.html
46-
47-
cat <<-END_VERSIONS > versions.yml
48-
"${task.process}":
49-
r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
50-
END_VERSIONS
5141
"""
5242
}

‎modules/nf-core/shinyngs/staticdifferential/meta.yml‎

Lines changed: 21 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -73,13 +73,28 @@ output:
7373
Meta-keyed tuple containing an HTML output for a volcano plot built
7474
from the differential result table.
7575
ontologies: []
76+
versions_shinyngs:
77+
- - ${task.process}:
78+
type: string
79+
description: The name of the process
80+
- shinyngs:
81+
type: string
82+
description: The name of the tool
83+
- 'Rscript -e "library(shinyngs); cat(as.character(packageVersion(''shinyngs'')))"':
84+
type: eval
85+
description: The expression to obtain the version of the tool
86+
87+
topics:
7688
versions:
77-
- versions.yml:
78-
type: file
79-
description: File containing software versions
80-
pattern: "versions.yml"
81-
ontologies:
82-
- edam: http://edamontology.org/format_3750 # YAML
89+
- - ${task.process}:
90+
type: string
91+
description: The name of the process
92+
- shinyngs:
93+
type: string
94+
description: The name of the tool
95+
- 'Rscript -e "library(shinyngs); cat(as.character(packageVersion(''shinyngs'')))"':
96+
type: eval
97+
description: The expression to obtain the version of the tool
8398
authors:
8499
- "@pinin4fjords"
85100
maintainers:

‎modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -62,7 +62,7 @@ nextflow_process {
6262
{ assert snapshot(
6363
file(process.out.volcanos_png[0][1]).name, //assert unstable file
6464
process.out.volcanos_html,
65-
process.out.versions
65+
process.out.findAll { key, val -> key.startsWith('versions') }
6666
).match()
6767
}
6868
)

‎modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap‎

Lines changed: 28 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -5,15 +5,21 @@
55
[
66

77
],
8-
[
9-
"versions.yml:md5,a71d1d5f6a15f9fefd34ca0ada81842b"
10-
]
8+
{
9+
"versions_shinyngs": [
10+
[
11+
"SHINYNGS_STATICDIFFERENTIAL",
12+
"shinyngs",
13+
"2.4.0"
14+
]
15+
]
16+
}
1117
],
18+
"timestamp": "2026-04-16T19:22:01.222412911",
1219
"meta": {
13-
"nf-test": "0.9.3",
14-
"nextflow": "25.10.0"
15-
},
16-
"timestamp": "2025-12-01T17:45:23.17214359"
20+
"nf-test": "0.9.4",
21+
"nextflow": "25.10.4"
22+
}
1723
},
1824
"stub": {
1925
"content": [
@@ -43,10 +49,18 @@
4349
]
4450
],
4551
"2": [
46-
"versions.yml:md5,a71d1d5f6a15f9fefd34ca0ada81842b"
52+
[
53+
"SHINYNGS_STATICDIFFERENTIAL",
54+
"shinyngs",
55+
"2.4.0"
56+
]
4757
],
48-
"versions": [
49-
"versions.yml:md5,a71d1d5f6a15f9fefd34ca0ada81842b"
58+
"versions_shinyngs": [
59+
[
60+
"SHINYNGS_STATICDIFFERENTIAL",
61+
"shinyngs",
62+
"2.4.0"
63+
]
5064
],
5165
"volcanos_html": [
5266
[
@@ -74,10 +88,10 @@
7488
]
7589
}
7690
],
91+
"timestamp": "2026-04-16T19:22:14.145006911",
7792
"meta": {
78-
"nf-test": "0.9.3",
79-
"nextflow": "25.10.0"
80-
},
81-
"timestamp": "2025-12-01T17:45:36.887175944"
93+
"nf-test": "0.9.4",
94+
"nextflow": "25.10.4"
95+
}
8296
}
8397
}

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