diff --git a/modules/nf-core/ribodetector/environment.gpu.yml b/modules/nf-core/ribodetector/environment.gpu.yml index 221fb0a83086..af9b9052ddad 100644 --- a/modules/nf-core/ribodetector/environment.gpu.yml +++ b/modules/nf-core/ribodetector/environment.gpu.yml @@ -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" diff --git a/modules/nf-core/ribodetector/main.nf b/modules/nf-core/ribodetector/main.nf index f85b86a62d40..880247c185b8 100644 --- a/modules/nf-core/ribodetector/main.nf +++ b/modules/nf-core/ribodetector/main.nf @@ -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) @@ -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 diff --git a/modules/nf-core/ribodetector/meta.yml b/modules/nf-core/ribodetector/meta.yml index 76d8f5c8774b..06ec28163578 100644 --- a/modules/nf-core/ribodetector/meta.yml +++ b/modules/nf-core/ribodetector/meta.yml @@ -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: @@ -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" diff --git a/modules/nf-core/ribodetector/tests/main.gpu.nf.test.snap b/modules/nf-core/ribodetector/tests/main.gpu.nf.test.snap index 89a71d3145c8..46c79b54c48a 100644 --- a/modules/nf-core/ribodetector/tests/main.gpu.nf.test.snap +++ b/modules/nf-core/ribodetector/tests/main.gpu.nf.test.snap @@ -8324,6 +8324,13 @@ "SRR5665260.1.998901/2" ], { + "versions_cuda": [ + [ + "RIBODETECTOR", + "cuda", + "11.2" + ] + ], "versions_ribodetector": [ [ "RIBODETECTOR", @@ -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": { @@ -8370,6 +8377,13 @@ "0.3.3" ] ], + "3": [ + [ + "RIBODETECTOR", + "cuda", + "11.2" + ] + ], "fastq": [ [ { @@ -8391,6 +8405,13 @@ "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "versions_cuda": [ + [ + "RIBODETECTOR", + "cuda", + "11.2" + ] + ], "versions_ribodetector": [ [ "RIBODETECTOR", @@ -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" } } -} +} \ No newline at end of file diff --git a/modules/nf-core/ribodetector/tests/main.nf.test.snap b/modules/nf-core/ribodetector/tests/main.nf.test.snap index cc0a213879a9..1cefad26360f 100644 --- a/modules/nf-core/ribodetector/tests/main.nf.test.snap +++ b/modules/nf-core/ribodetector/tests/main.nf.test.snap @@ -8324,6 +8324,13 @@ "SRR5665260.1.998901/2" ], { + "versions_cuda": [ + [ + "RIBODETECTOR", + "cuda", + "no CUDA available" + ] + ], "versions_ribodetector": [ [ "RIBODETECTOR", @@ -8370,6 +8377,13 @@ "0.3.3" ] ], + "3": [ + [ + "RIBODETECTOR", + "cuda", + "no CUDA available" + ] + ], "fastq": [ [ { @@ -8391,6 +8405,13 @@ "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "versions_cuda": [ + [ + "RIBODETECTOR", + "cuda", + "no CUDA available" + ] + ], "versions_ribodetector": [ [ "RIBODETECTOR",