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fix: unpin ribodetector GPU from pytorch-gpu=1.11.0 (__cuda workaround no longer needed) #11258

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Merged
pinin4fjords merged 7 commits into from
Apr 22, 2026
Merged

fix: unpin ribodetector GPU from pytorch-gpu=1.11.0 (__cuda workaround no longer needed) #11258

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aa23854
fix: update ribodetector GPU container to CUDA 12.x
pinin4fjords Apr 22, 2026
9462ebb
fix(ribodetector): pin pytorch-gpu=2.1.0 + cuda-version=11.2 for wide…
pinin4fjords Apr 22, 2026
b4da63c
test(ribodetector): add versions_cuda entries to existing CPU snapshot
pinin4fjords Apr 22, 2026
5290440
test(ribodetector): fix versions_cuda key order in CPU snapshot
pinin4fjords Apr 22, 2026
4c11604
Merge branch 'master' into fix/ribodetector-containers-only
pinin4fjords Apr 22, 2026
b822b65
[automated] Update gpu snapshot
nf-core-bot Apr 22, 2026
eb16c2f
fix(ribodetector): use descriptive cuda fallback string on non-GPU path
pinin4fjords Apr 22, 2026
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3 changes: 2 additions & 1 deletion modules/nf-core/ribodetector/environment.gpu.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,5 @@ channels:
- bioconda
dependencies:
- "bioconda::ribodetector=0.3.3"
- "conda-forge::pytorch-gpu=1.11.0"
- "conda-forge::pytorch-gpu=2.1.0"
- "conda-forge::cuda-version=11.2"
5 changes: 3 additions & 2 deletions modules/nf-core/ribodetector/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process RIBODETECTOR {

conda "${ task.accelerator ? "${moduleDir}/environment.gpu.yml" : "${moduleDir}/environment.yml" }"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
(task.accelerator ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/ebcccef2cd8b4c10d4bbd8fce542b46502b7817115cb144b9566792b0aac9bc0/data' : 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/463b8ad941e7f1f2decef20844d666c1c8ac233e166d2bc766164c4a93905a3c/data') :
(task.accelerator ? 'community.wave.seqera.io/library/ribodetector_pytorch-gpu:f2d45093d4093307' : 'community.wave.seqera.io/library/ribodetector:0.3.3--ad3d7071e408b502') }"
(task.accelerator ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/51100097fc2e31d7b78074bc954774f77726099220e820382e939278817a66da/data' : 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/463b8ad941e7f1f2decef20844d666c1c8ac233e166d2bc766164c4a93905a3c/data') :
(task.accelerator ? 'community.wave.seqera.io/library/ribodetector_pytorch-gpu_cuda-version:fa9183da731515ea' : 'community.wave.seqera.io/library/ribodetector:0.3.3--ad3d7071e408b502') }"

input:
tuple val(meta), path(fastq)
Expand All @@ -15,6 +15,7 @@ process RIBODETECTOR {
tuple val(meta), path("*.nonrna*.fastq.gz"), emit: fastq
tuple val(meta), path("*.log") , emit: log
tuple val("${task.process}"), val('ribodetector'), eval('ribodetector --version | sed "s/ribodetector //"'), emit: versions_ribodetector, topic: versions
tuple val("${task.process}"), val('cuda'), eval('python -c "import torch; print(torch.version.cuda or \'no CUDA available\')"'), emit: versions_cuda, topic: versions

when:
task.ext.when == null || task.ext.when
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19 changes: 19 additions & 0 deletions modules/nf-core/ribodetector/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,16 @@ output:
- ribodetector --version | sed "s/ribodetector //":
type: eval
description: The expression to obtain the version of the tool
versions_cuda:
- - ${task.process}:
type: string
description: Name of the process
- cuda:
type: string
description: Name of the runtime
- python -c "import torch; print(torch.version.cuda or 'no CUDA available')":
type: eval
description: CUDA version bundled with the task's pytorch build, or `no CUDA available` on the non-GPU path

topics:
versions:
Expand All @@ -88,6 +98,15 @@ topics:
- ribodetector --version | sed "s/ribodetector //":
type: eval
description: The expression to obtain the version of the tool
- - ${task.process}:
type: string
description: Name of the process
- cuda:
type: string
description: Name of the runtime
- python -c "import torch; print(torch.version.cuda or 'no CUDA available')":
type: eval
description: CUDA version bundled with the task's pytorch build, or `no CUDA available` on the non-GPU path

authors:
- "@maxibor"
Expand Down
31 changes: 26 additions & 5 deletions modules/nf-core/ribodetector/tests/main.gpu.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8324,6 +8324,13 @@
"SRR5665260.1.998901/2"
],
{
"versions_cuda": [
[
"RIBODETECTOR",
"cuda",
"11.2"
]
],
"versions_ribodetector": [
[
"RIBODETECTOR",
Expand All @@ -8333,10 +8340,10 @@
]
}
],
"timestamp": "2026-04-14T11:11:46.109723883",
"timestamp": "2026-04-22T13:15:51.198102608",
"meta": {
"nf-test": "0.9.5",
"nextflow": "25.10.4"
"nextflow": "25.10.2"
}
},
"ribodetector - GPU stub rnaseq PE input": {
Expand Down Expand Up @@ -8370,6 +8377,13 @@
"0.3.3"
]
],
"3": [
[
"RIBODETECTOR",
"cuda",
"11.2"
]
],
"fastq": [
[
{
Expand All @@ -8391,6 +8405,13 @@
"test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions_cuda": [
[
"RIBODETECTOR",
"cuda",
"11.2"
]
],
"versions_ribodetector": [
[
"RIBODETECTOR",
Expand All @@ -8400,10 +8421,10 @@
]
}
],
"timestamp": "2026-04-14T11:11:53.692394926",
"timestamp": "2026-04-22T13:16:06.36963835",
"meta": {
"nf-test": "0.9.5",
"nextflow": "25.10.4"
"nextflow": "25.10.2"
}
}
}
}
21 changes: 21 additions & 0 deletions modules/nf-core/ribodetector/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8324,6 +8324,13 @@
"SRR5665260.1.998901/2"
],
{
"versions_cuda": [
[
"RIBODETECTOR",
"cuda",
"no CUDA available"
]
],
"versions_ribodetector": [
[
"RIBODETECTOR",
Expand Down Expand Up @@ -8370,6 +8377,13 @@
"0.3.3"
]
],
"3": [
[
"RIBODETECTOR",
"cuda",
"no CUDA available"
]
],
"fastq": [
[
{
Expand All @@ -8391,6 +8405,13 @@
"test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions_cuda": [
[
"RIBODETECTOR",
"cuda",
"no CUDA available"
]
],
"versions_ribodetector": [
[
"RIBODETECTOR",
Expand Down
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