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🔧 update image and bioconda container for VueGen to latest version #9201

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fd604a1
🔧 update image and bioconda container to latest version
enryH Oct 16, 2025
a1d39a8
✅ update test snapshots
enryH Oct 16, 2025
3b4ebd1
Merge branch 'master' into update_vuegen
famosab Oct 17, 2025
5eb02c4
:bug: fix display of version of vuegen
enryH Oct 20, 2025
8de97ed
Merge branch 'master' into update_vuegen
famosab Oct 20, 2025
9b17dc0
:art: display versions.yml content in snapshots
enryH Oct 20, 2025
0956008
Merge branch 'master' into update_vuegen
enryH Oct 22, 2025
b8e8add
🔧 add Dockerfile to install lastet PyPI vuegen version
enryH Oct 22, 2025
6bf04c9
🚧 add wave containers
enryH Oct 22, 2025
9fe09f6
:fire: remove README again
enryH Oct 24, 2025
d9f4c67
Merge branch 'master' into update_vuegen
enryH Oct 24, 2025
3493280
:fire: remove Dockerfile again
enryH Oct 24, 2025
e9b110f
Merge branch 'master' into update_vuegen
enryH Oct 28, 2025
f25c416
🚧 try to follow Mahesh's advice
enryH Oct 28, 2025
15c1836
Merge branch 'master' into update_vuegen
enryH Oct 28, 2025
f71f78c
:bug: add explicit cache directory
enryH Oct 29, 2025
68f79c7
Merge branch 'master' into update_vuegen
enryH Oct 29, 2025
2791af4
🔧 bump to Python 3.12 and remove channel prefix
enryH Oct 29, 2025
58ef775
:wrench: specify singularity image with https
enryH Oct 29, 2025
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2 changes: 1 addition & 1 deletion modules/nf-core/vuegen/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,5 +4,5 @@ channels:
- bioconda
- conda-forge
dependencies:
- bioconda::vuegen=0.3.2
- bioconda::vuegen=0.5.1
- python=3.11
6 changes: 3 additions & 3 deletions modules/nf-core/vuegen/main.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
process VUEGEN {
label 'process_single'
conda "${moduleDir}/environment.yml"
container "dtu_biosustain_dsp/vuegen:v0.3.2-nextflow"
container "dtu_biosustain_dsp/vuegen:v0.5.1-nextflow"
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Can we get this container moved to the nf-core quay.io please?

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Do I need special permission? are there instructions for moving it?

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a core member (like me) needs to do it. could you prepare it according to step 2 here please https://nf-co.re/docs/checklists/community_governance/core_team#making-custom-docker-containers-for-modules

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ok. We have a Dockerfile and I will add it to the module here, see: Multiomics-Analytics-Group/nf-vuegen#1

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I see that most core modules 'only' have a conda environment file. Would you then auto-build the docker container (I like wave, but so far i think one has to either use wave or docker, and cannot 'just' use wave for modules which do not have their own docker images)

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if you have everything in a conda env file, you can just use seqera containers to build docker and singularity images: https://nf-co.re/docs/tutorials/nf-core_components/using_seqera_containers

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done.


input:
val input_type
Expand Down Expand Up @@ -36,7 +36,7 @@ process VUEGEN {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
vuegen: \$( vuegen --version | sed -e "s/vuegen //g" )
vuegen: \$( python -c "import vuegen; print(vuegen.__version__)" )
END_VERSIONS
"""

Expand All @@ -48,7 +48,7 @@ process VUEGEN {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
vuegen: \$( vuegen --version | sed -e "s/vuegen //g" )
vuegen: \$( python -c "import vuegen; print(vuegen.__version__)" )
END_VERSIONS
"""
}
10 changes: 5 additions & 5 deletions modules/nf-core/vuegen/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ nextflow_process {
"Static_Plots.py": path(process.out.output_folder[0] + "/sections/Plots/Static_Plots.py")
.readLines()[0..3].sort().join('\n').md5()
],
versions: process.out.versions
versions: path(process.out.versions[0]).yaml,
]).match()
}
)
Expand Down Expand Up @@ -80,7 +80,7 @@ nextflow_process {
"quarto_report.qmd": path(process.out.output_folder[0] + "/quarto_report.qmd")
.readLines()[0..3].join('\n').md5()
],
versions: process.out.versions
versions: path(process.out.versions[0]).yaml
]).match()
}
)
Expand Down Expand Up @@ -111,7 +111,7 @@ nextflow_process {
"quarto_report.qmd": path(process.out.output_folder[0] + "/quarto_report.qmd")
.readLines()[0..3].sort().join('\n').md5()
],
versions: process.out.versions
versions: path(process.out.versions[0]).yaml,
]).match()
}
)
Expand All @@ -138,10 +138,10 @@ nextflow_process {
assert snapshot(
process.out.output_folder.collect { file(it).getName() } +
process.out.output_files.collect { file(it).getName() },
versions: process.out.versions
versions: path(process.out.versions[0]).yaml,
).match()
}
)
}
}
}
}
58 changes: 33 additions & 25 deletions modules/nf-core/vuegen/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,19 +2,21 @@
"vuegen - directory (HTML report) -stub": {
"content": [
{
"versions": [
"versions.yml:md5,c3e7ebc433dcacf3d15e1113fd44f5ec"
]
"versions": {
"VUEGEN": {
"vuegen": "0.5.1"
}
}
},
[
"report"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "24.10.6"
},
"timestamp": "2025-04-22T09:34:45.900956"
"timestamp": "2025-10-20T13:25:42.669804"
},
"vuegen - directory (HTML report)": {
"content": [
Expand All @@ -24,16 +26,18 @@
"quarto_report.html": "0129d189059f27b3d2ff6f328cd18ef9",
"quarto_report.qmd": "e60a379de892055748e4597f9d8c656c"
},
"versions": [
"versions.yml:md5,c3e7ebc433dcacf3d15e1113fd44f5ec"
]
"versions": {
"VUEGEN": {
"vuegen": "0.5.1"
}
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "24.10.6"
},
"timestamp": "2025-04-22T09:04:23.56469"
"timestamp": "2025-10-20T13:24:59.558083"
},
"vuegen - directory (PDF report)": {
"content": [
Expand All @@ -43,37 +47,41 @@
"quarto_report.pdf": true,
"quarto_report.qmd": "c447088ca2a435acf926ec5e95c51265"
},
"versions": [
"versions.yml:md5,c3e7ebc433dcacf3d15e1113fd44f5ec"
]
"versions": {
"VUEGEN": {
"vuegen": "0.5.1"
}
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "24.10.6"
},
"timestamp": "2025-04-22T09:05:54.139709"
"timestamp": "2025-10-20T13:25:37.140787"
},
"vuegen - directory (Streamlit report)": {
"content": [
{
"output_folder": true,
"output_files": {
"Homepage.py": "Homepage.py:md5,483a41696c225663772d68ff2d664493",
"report_manager.py": "report_manager.py:md5,ed15eefa722b7a2f08cca016c0c8e28d",
"All_Formats.py": "e2a56e761eb537da8f9809cbc0b63a9d",
"Interactive_Plots.py": "3198216240ef9b86d5b1ed722bd9b31c",
"Static_Plots.py": "931fd04e2e49cb14d169747b6d5bbd1e"
"Homepage.py": "Homepage.py:md5,a46395bbdfb127463d51d8f601f2ad83",
"report_manager.py": "report_manager.py:md5,a683071ba8bc6e371c8617ef9c3fb84e",
"All_Formats.py": "1f61acc3ca34f6ff941c109d93570815",
"Interactive_Plots.py": "4857dc511178812e93c2037c8bbe04f4",
"Static_Plots.py": "ae9c2e46ae9a9e0e5e98fcce87cd7f80"
},
"versions": [
"versions.yml:md5,c3e7ebc433dcacf3d15e1113fd44f5ec"
]
"versions": {
"VUEGEN": {
"vuegen": "0.5.1"
}
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "24.10.6"
},
"timestamp": "2025-04-22T09:03:48.375488"
"timestamp": "2025-10-20T13:19:47.56244"
}
}
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