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viennarna: Update to version 2.7.2 and to use Seqera containers #13353

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Merged
renatosantos98 merged 6 commits into from
Oct 27, 2026
Merged

viennarna: Update to version 2.7.2 and to use Seqera containers #13353

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adc5162
viennarna: Update to use Seqera containers
renatosantos98 Oct 16, 2026
a37e138
Merge branch 'nf-core:master' into viennarna_seq_containers
renatosantos98 Oct 16, 2026
735fadf
viennarna/rnafold: Remove unstableKeys from snapshot assertion in test
renatosantos98 Oct 16, 2026
4885779
Merge branch 'nf-core:master' into viennarna_seq_containers
renatosantos98 Oct 26, 2026
da3ca7c
Update viennarna to version 2.7.2 in environment files
renatosantos98 Oct 27, 2026
6a155fc
Merge branch 'nf-core:master' into viennarna_seq_containers
renatosantos98 Oct 27, 2026
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475 changes: 475 additions & 0 deletions modules/nf-core/viennarna/rnacofold/.conda-lock/linux_amd64-bd-6e8b02540b675a6c_1.txt
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444 changes: 444 additions & 0 deletions modules/nf-core/viennarna/rnacofold/.conda-lock/linux_arm64-bd-57c349bf20a41eac_1.txt
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2 changes: 1 addition & 1 deletion modules/nf-core/viennarna/rnacofold/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::viennarna=2.6.4
- bioconda::viennarna=2.7.2
6 changes: 3 additions & 3 deletions modules/nf-core/viennarna/rnacofold/main.nf
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Expand Up @@ -3,9 +3,9 @@ process VIENNARNA_RNACOFOLD {
label 'process_low'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/viennarna:2.6.4--py310pl5321h6cc9453_1':
'quay.io/biocontainers/viennarna:2.6.4--py310pl5321h6cc9453_1' }"
container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/1048b2d5571e2deab1e43e6629bbe4e6c7e9d8780b9dfbf0d3e0f44adb131021/data'
: 'community.wave.seqera.io/library/viennarna:2.7.2--6e8b02540b675a6c'}"

input:
tuple val(meta), path(rnacofold_fasta)
Expand Down
30 changes: 26 additions & 4 deletions modules/nf-core/viennarna/rnacofold/meta.yml
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Expand Up @@ -54,8 +54,7 @@ output:
e.g. [ id:'test', single_end:false ]
- "*.csv":
type: file
description: The CSV Output of RNAcofold that has the predicted
structure and energies
description: The CSV Output of RNAcofold that has the predicted structure and energies
pattern: "*.{csv}"
ontologies:
- edam: http://edamontology.org/format_3752
Expand All @@ -67,8 +66,7 @@ output:
e.g. [ id:'test', single_end:false ]
- "*.ps":
type: file
description: The text Output of RNAfold that contains the predicted
secondary structure in postscript format
description: The text Output of RNAfold that contains the predicted secondary structure in postscript format
pattern: "*.{ps}"
ontologies: []
versions_rnacofold:
Expand Down Expand Up @@ -96,3 +94,27 @@ authors:
- "@kokul-atx"
maintainers:
- "@kokul-atx"
containers:
docker:
linux/amd64:
name: community.wave.seqera.io/library/viennarna:2.7.2--6e8b02540b675a6c
build_id: bd-6e8b02540b675a6c_1
scan_id: sc-a66ad13df50b0c06_1
linux/arm64:
name: community.wave.seqera.io/library/viennarna:2.7.2--57c349bf20a41eac
build_id: bd-57c349bf20a41eac_1
scan_id: sc-7bc811c203663145_1
singularity:
linux/arm64:
name: oras://community.wave.seqera.io/library/viennarna:2.7.2--53f2d9d6676a2a66
build_id: bd-53f2d9d6676a2a66_1
https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ab/ab295700229a0167197d24bc8dbfaccd4d38221b6ec1d498436e9d5791fcc107/data
linux/amd64:
name: oras://community.wave.seqera.io/library/viennarna:2.7.2--8731ab37e9c410b1
build_id: bd-8731ab37e9c410b1_1
https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/1048b2d5571e2deab1e43e6629bbe4e6c7e9d8780b9dfbf0d3e0f44adb131021/data
conda:
linux/amd64:
lock_file: modules/nf-core/viennarna/rnacofold/.conda-lock/linux_amd64-bd-6e8b02540b675a6c_1.txt
linux/arm64:
lock_file: modules/nf-core/viennarna/rnacofold/.conda-lock/linux_arm64-bd-57c349bf20a41eac_1.txt
12 changes: 6 additions & 6 deletions modules/nf-core/viennarna/rnacofold/tests/main.nf.test.snap
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Expand Up @@ -22,15 +22,15 @@
[
"VIENNARNA_RNACOFOLD",
"RNAcofold",
"2.6.4"
"2.7.2"
]
]
}
],
"timestamp": "2026-06-18T06:35:19.517723545",
"timestamp": "2026-10-27T00:51:08.620150031",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
"nextflow": "26.10.3"
}
},
"rnacofold - fasta": {
Expand Down Expand Up @@ -60,15 +60,15 @@
[
"VIENNARNA_RNACOFOLD",
"RNAcofold",
"2.6.4"
"2.7.2"
]
]
}
],
"timestamp": "2026-06-18T06:41:26.334515517",
"timestamp": "2026-10-27T00:51:04.736845949",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
"nextflow": "26.10.3"
}
}
}
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