Update llamacpppython/run module for using 0.3.28 version

modules/nf-core/llamacpppython/run/environment.gpu.yml

@@ -3,9 +3,5 @@
 channels:
   - conda-forge
 dependencies:
-  - python=3.11
-  - pip
-  - "conda-forge::cuda-version=12.4"
-  - "conda-forge::cuda-runtime"
-  - pip:
-      - "https://github.com/abetlen/llama-cpp-python/releases/download/v0.3.16-cu124/llama_cpp_python-0.3.16-cp311-cp311-linux_x86_64.whl"
+  - llama-cpp-python=0.3.28
+  - llama.cpp=9574=*cuda*

modules/nf-core/llamacpppython/run/environment.yml

@@ -2,6 +2,5 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
-  - bioconda
 dependencies:
-  - conda-forge::llama-cpp-python=0.3.16
+  - llama-cpp-python=0.3.28

modules/nf-core/llamacpppython/run/main.nf

@@ -4,8 +4,8 @@ process LLAMACPPPYTHON_RUN {
 
     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/sha256/9f/9f5c3807fc8d9a8c28cef653f377cec46d26097ad157571001316dd8ca196fb4/data' : 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3c/3c1e6f266b077ae89b341bf921b59a3d5d382104c3775725a814bd68f064541e/data') :
-        (task.accelerator ? 'community.wave.seqera.io/library/python_pip_cuda-version_cuda-runtime:202c39541466fecd' : 'community.wave.seqera.io/library/llama-cpp-python:0.3.16--b351398cd0ea7fc5') }"
+        (task.accelerator ? 'oras://community.wave.seqera.io/library/llama-cpp-python_llama.cpp:d44fd00c4d90dbdb' : 'oras://community.wave.seqera.io/library/llama-cpp-python:0.3.28--50ab38de95fd7615') :
+        (task.accelerator ? 'community.wave.seqera.io/library/llama-cpp-python_llama.cpp:d81eb47f02f98bad' : 'community.wave.seqera.io/library/llama-cpp-python:0.3.28--d6b1d777bf1649d9') }"
 
     input:
     tuple val(meta), path(prompt_file), path(gguf_model)

modules/nf-core/llamacpppython/run/tests/main.gpu.nf.test

@@ -61,7 +61,8 @@ nextflow_process {
                     process.out.output[0][0],
                     file(process.out.output[0][1]).name,
                     file(process.out.output[0][1]).size() > 0,
-                    process.out.findAll { key, val -> key.startsWith('versions') }
+                    process.out.findAll { key, val -> key.startsWith('versions') },
+                    process.out.versions_llama_cpp_python.collect { path(it).yaml.values().first() }
                 ).match() }
             )
         }
@@ -107,7 +108,8 @@ nextflow_process {
                     process.out.output.size(),
                     process.out.output[0][0],
                     file(process.out.output[0][1]).name,
-                    process.out.findAll { key, val -> key.startsWith('versions') }
+                    process.out.findAll { key, val -> key.startsWith('versions') },
+                    process.out.versions_llama_cpp_python.collect { path(it).yaml.values().first() }
                 ).match() }
             )
         }

modules/nf-core/llamacpppython/run/tests/main.gpu.nf.test.snap

@@ -8,14 +8,20 @@
             "test_run.txt",
             {
                 "versions_llama_cpp_python": [
-                    "versions.yml:md5,3650e9ce14ab350b69387f6631b57885"
+                    "versions.yml:md5,e1da69d545e098db89cc40b726cb4627"
                 ]
-            }
+            },
+            [
+                {
+                    "llama-cpp-python": "0.3.28",
+                    "cuda": "no CUDA available"
+                }
+            ]
         ],
-        "timestamp": "2026-04-21T13:52:56.739988372",
+        "timestamp": "2026-06-12T18:48:36.516586462",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.3"
         }
     },
     "llamacpppython/run - GPU run inference with downloaded gguf model": {
@@ -28,14 +34,20 @@
             true,
             {
                 "versions_llama_cpp_python": [
-                    "versions.yml:md5,28ef3c6aa93df0de54e66c13cc9db845"
+                    "versions.yml:md5,addfc2cdc4f4ad37323d3bbd8b0f443f"
                 ]
-            }
+            },
+            [
+                {
+                    "llama-cpp-python": "0.3.28",
+                    "cuda": 13.0
+                }
+            ]
         ],
-        "timestamp": "2026-04-21T13:52:48.948862428",
+        "timestamp": "2026-06-12T18:48:25.857178068",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.3"
         }
     }
 }

modules/nf-core/llamacpppython/run/tests/main.nf.test

@@ -60,7 +60,8 @@ nextflow_process {
                     process.out.output[0][0],
                     file(process.out.output[0][1]).name,
                     file(process.out.output[0][1]).size() > 0,
-                    process.out.findAll { key, val -> key.startsWith('versions') }
+                    process.out.findAll { key, val -> key.startsWith('versions') },
+                    process.out.versions_llama_cpp_python.collect { path(it).yaml.values().first() }
                 ).match() }
             )
         }
@@ -106,7 +107,8 @@ nextflow_process {
                     process.out.output.size(),
                     process.out.output[0][0],
                     file(process.out.output[0][1]).name,
-                    process.out.findAll { key, val -> key.startsWith('versions') }
+                    process.out.findAll { key, val -> key.startsWith('versions') },
+                    process.out.versions_llama_cpp_python.collect { path(it).yaml.values().first() }
                 ).match() }
             )
         }

modules/nf-core/llamacpppython/run/tests/main.nf.test.snap

@@ -9,14 +9,20 @@
             true,
             {
                 "versions_llama_cpp_python": [
-                    "versions.yml:md5,3650e9ce14ab350b69387f6631b57885"
+                    "versions.yml:md5,e1da69d545e098db89cc40b726cb4627"
                 ]
-            }
+            },
+            [
+                {
+                    "llama-cpp-python": "0.3.28",
+                    "cuda": "no CUDA available"
+                }
+            ]
         ],
-        "timestamp": "2026-04-14T22:59:52.532384543",
+        "timestamp": "2026-06-12T16:40:03.537996441",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.3"
         }
     },
     "stub - run inference with json prompt": {
@@ -28,14 +34,20 @@
             "test_run.txt",
             {
                 "versions_llama_cpp_python": [
-                    "versions.yml:md5,3650e9ce14ab350b69387f6631b57885"
+                    "versions.yml:md5,e1da69d545e098db89cc40b726cb4627"
                 ]
-            }
+            },
+            [
+                {
+                    "llama-cpp-python": "0.3.28",
+                    "cuda": "no CUDA available"
+                }
+            ]
         ],
-        "timestamp": "2026-04-14T22:59:56.61647329",
+        "timestamp": "2026-06-12T16:40:07.65398849",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.3"
         }
     }
 }