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Updated shinyngs containers and nftest snaps #7323

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merged 5 commits into from
Jan 17, 2025
Merged

Updated shinyngs containers and nftest snaps #7323

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c9895dd
Updated shinyngs containers and nftest snaps
nschcolnicov Jan 16, 2025
144fd56
Updated conda versions
nschcolnicov Jan 16, 2025
2f32f10
Remove r from versions.yml
nschcolnicov Jan 17, 2025
7e71f5c
Merge branch 'master' of https://github.com/nf-core/modules into bump…
nschcolnicov Jan 17, 2025
5cf46fe
Remove unstable volcano.png file from assertion
nschcolnicov Jan 17, 2025
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3 changes: 2 additions & 1 deletion modules/nf-core/shinyngs/app/environment.yml
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Expand Up @@ -2,4 +2,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::r-shinyngs=2.0.0
- bioconda::r-shinyngs=2.1.0
- conda-forge::r-base=4.4.2
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I assume this pin is there to fix the snapshots.

Actually, I think we should just take the R version out of the version outputs from the modules. I hadn't appreciated when I wrote the modules that it would be disruptive, and I don't think there's a good reason to pin R otherwise.

We will in due course have lockfiles in nf-core to cover the real use case for this sort of thing.

4 changes: 2 additions & 2 deletions modules/nf-core/shinyngs/app/main.nf
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Expand Up @@ -15,8 +15,8 @@ process SHINYNGS_APP {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/r-shinyngs:2.0.0--r43hdfd78af_0' :
'biocontainers/r-shinyngs:2.0.0--r43hdfd78af_0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/97/971684ed03cda2689eea7db9e7f2ee74d079ddd74e3a3baac31e958eea6feb0e/data' :
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Nice- was going to suggest this

'community.wave.seqera.io/library/r-shinyngs:2.1.0--09e258eb60cb225f' }"

input:
tuple val(meta), path(sample), path(feature_meta), path(assay_files) // Experiment-level info
Expand Down
24 changes: 12 additions & 12 deletions modules/nf-core/shinyngs/app/tests/main.nf.test.snap
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Expand Up @@ -4,41 +4,41 @@
"data.rds",
"app.R:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"versions.yml:md5,a6c3af4b2fd261b4049c92449ea6bb4d"
"versions.yml:md5,8e8f77fd5f860fb3e8123f266c0c450b"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-06-25T09:43:49.880332"
"timestamp": "2025-01-16T20:12:57.965636745"
},
"mouse - multi matrix": {
"content": [
"data.rds",
"app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
[
"versions.yml:md5,a6c3af4b2fd261b4049c92449ea6bb4d"
"versions.yml:md5,8e8f77fd5f860fb3e8123f266c0c450b"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-06-25T09:43:15.455356"
"timestamp": "2025-01-16T20:12:25.659843541"
},
"mouse - single matrix": {
"content": [
"data.rds",
"app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
[
"versions.yml:md5,a6c3af4b2fd261b4049c92449ea6bb4d"
"versions.yml:md5,8e8f77fd5f860fb3e8123f266c0c450b"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-06-25T09:43:35.309081"
"timestamp": "2025-01-16T20:12:44.933479752"
}
}
4 changes: 2 additions & 2 deletions modules/nf-core/shinyngs/staticdifferential/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::r-shinyngs=2.0.0
- conda-forge::r-base=4.3.3
- bioconda::r-shinyngs=2.1.0
- conda-forge::r-base=4.4.2
6 changes: 3 additions & 3 deletions modules/nf-core/shinyngs/staticdifferential/main.nf
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Expand Up @@ -4,8 +4,8 @@ process SHINYNGS_STATICDIFFERENTIAL {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2b/2b43cb5832431a3d581f3abdca0f5d45fa814b8a4b2c4e49f12296d2e07629fd/data' :
'community.wave.seqera.io/library/r-shinyngs:2.0.0--feeacac14bcf4bb0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/97/971684ed03cda2689eea7db9e7f2ee74d079ddd74e3a3baac31e958eea6feb0e/data' :
'community.wave.seqera.io/library/r-shinyngs:2.1.0--09e258eb60cb225f' }"

input:
tuple val(meta), path(differential_result) // Differential info: contrast and differential stats
Expand Down Expand Up @@ -37,7 +37,7 @@ process SHINYNGS_STATICDIFFERENTIAL {
r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: meta.id
"""
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12 changes: 6 additions & 6 deletions modules/nf-core/shinyngs/staticdifferential/tests/main.nf.test.snap
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Expand Up @@ -18,10 +18,10 @@

],
"2": [
"versions.yml:md5,907105596993b0b0eda8989fba5a3a29"
"versions.yml:md5,45c5f38af38a536b8a0869946c746adf"
],
"versions": [
"versions.yml:md5,907105596993b0b0eda8989fba5a3a29"
"versions.yml:md5,45c5f38af38a536b8a0869946c746adf"
],
"volcanos_html": [

Expand All @@ -44,7 +44,7 @@
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-12-26T16:03:53.372133087"
"timestamp": "2025-01-16T20:13:20.440205437"
},
"stub": {
"content": [
Expand Down Expand Up @@ -74,10 +74,10 @@
]
],
"2": [
"versions.yml:md5,907105596993b0b0eda8989fba5a3a29"
"versions.yml:md5,45c5f38af38a536b8a0869946c746adf"
],
"versions": [
"versions.yml:md5,907105596993b0b0eda8989fba5a3a29"
"versions.yml:md5,45c5f38af38a536b8a0869946c746adf"
],
"volcanos_html": [
[
Expand Down Expand Up @@ -109,6 +109,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-12-26T16:04:08.867324031"
"timestamp": "2025-01-16T20:13:33.841282396"
}
}
3 changes: 2 additions & 1 deletion modules/nf-core/shinyngs/staticexploratory/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::r-shinyngs=2.0.0
- bioconda::r-shinyngs=2.1.0
- conda-forge::r-base=4.4.2
4 changes: 2 additions & 2 deletions modules/nf-core/shinyngs/staticexploratory/main.nf
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Expand Up @@ -4,8 +4,8 @@ process SHINYNGS_STATICEXPLORATORY {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/r-shinyngs:2.0.0--r43hdfd78af_0' :
'biocontainers/r-shinyngs:2.0.0--r43hdfd78af_0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/97/971684ed03cda2689eea7db9e7f2ee74d079ddd74e3a3baac31e958eea6feb0e/data' :
'community.wave.seqera.io/library/r-shinyngs:2.1.0--09e258eb60cb225f' }"

input:
tuple val(meta), path(sample), path(feature_meta), path(assay_files)
Expand Down
32 changes: 16 additions & 16 deletions modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test.snap
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Expand Up @@ -8,14 +8,14 @@
"pca3d.png",
"sample_dendrogram.png",
[
"versions.yml:md5,e04025d7790ddfa09ba5bd719cfba8c7"
"versions.yml:md5,6a4a415b0aad7a9878674ff5102f31e8"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-06-25T10:24:53.456056"
"timestamp": "2025-01-16T20:14:07.293636493"
},
"mouse - defaults": {
"content": [
Expand All @@ -26,14 +26,14 @@
"pca3d.png",
"sample_dendrogram.png",
[
"versions.yml:md5,e04025d7790ddfa09ba5bd719cfba8c7"
"versions.yml:md5,6a4a415b0aad7a9878674ff5102f31e8"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-06-25T10:24:39.111271"
"timestamp": "2025-01-16T20:13:54.495198737"
},
"mouse - specify log": {
"content": [
Expand All @@ -44,14 +44,14 @@
"pca3d.png",
"sample_dendrogram.png",
[
"versions.yml:md5,e04025d7790ddfa09ba5bd719cfba8c7"
"versions.yml:md5,6a4a415b0aad7a9878674ff5102f31e8"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-06-25T10:25:14.646472"
"timestamp": "2025-01-16T20:14:27.861376263"
},
"mouse - html": {
"content": [
Expand All @@ -67,13 +67,13 @@
false,
false,
[
"versions.yml:md5,e04025d7790ddfa09ba5bd719cfba8c7"
"versions.yml:md5,6a4a415b0aad7a9878674ff5102f31e8"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-06-25T10:25:38.256352"
"timestamp": "2025-01-16T20:14:50.517212318"
}
}
4 changes: 2 additions & 2 deletions modules/nf-core/shinyngs/validatefomcomponents/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::r-shinyngs=2.0.0
- conda-forge::r-base=4.3.3
- bioconda::r-shinyngs=2.1.0
- conda-forge::r-base=4.4.2
4 changes: 2 additions & 2 deletions modules/nf-core/shinyngs/validatefomcomponents/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process SHINYNGS_VALIDATEFOMCOMPONENTS {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2b/2b43cb5832431a3d581f3abdca0f5d45fa814b8a4b2c4e49f12296d2e07629fd/data' :
'community.wave.seqera.io/library/r-shinyngs:2.0.0--feeacac14bcf4bb0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/97/971684ed03cda2689eea7db9e7f2ee74d079ddd74e3a3baac31e958eea6feb0e/data' :
'community.wave.seqera.io/library/r-shinyngs:2.1.0--09e258eb60cb225f' }"

input:
tuple val(meta), path(sample), path(assay_files)
Expand Down
33 changes: 33 additions & 0 deletions modules/nf-core/shinyngs/validatefomcomponents/tests/main.nf.test
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Expand Up @@ -43,6 +43,39 @@ nextflow_process {
}
}

test("test_yaml") {

when {
params{
observations_id_col = "sample"
features_id_col = "gene_id"

module_args = "--sample_id_col '${params.observations_id_col}' --feature_id_col '${params.features_id_col}'"
}
process {
"""
input[0] = [['id':'SRP254919'],
file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv", checkIfExists:true),
file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv", checkIfExists:true)
]
input[1] = [['id':'SRP254919'],
file(params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/Mus_musculus.anno.tsv", checkIfExists:true)
]
input[2] = [['id':'SRP254919'],
file("params.modules_testdata_base_path + "genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.yaml", checkIfExists:true)
]
"""
}
}

then {
assertAll (
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}

test("stub") {

options "-stub"
Expand Down
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