Amulety modules bump versions

.github/workflows/nf-test-gpu.yml

@@ -104,7 +104,11 @@ jobs:
   # Standard GPU tests (g4dn.xlarge - 4 vCPU, 16 GB RAM, T4 GPU)
   # Runs tests tagged "gpu" (20+ modules: parabricks, amulety, cellpose, etc.)
   nf-test-gpu:
-    runs-on: "runs-on=${{ github.run_id }}/family=g4dn.xlarge/image=ubuntu24-gpu-x64"
+    runs-on:
+      - runs-on=${{ github.run_id }}
+      - family=g4dn.xlarge
+      - image=ubuntu24-gpu-x64
+      - volume=40gb
     name: "GPU Test | g4dn.xlarge | ${{ matrix.profile }} | ${{ matrix.shard }}"
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.gpu_total_shards != '0' && needs.nf-test-changes.outputs.gpu_total_shards != '' }}

.github/workflows/nf-test.yml

@@ -93,6 +93,7 @@ jobs:
       - runs-on=${{ github.run_id }}
       - runner=4cpu-linux-${{ matrix.arch }}
       - image=ubuntu24-full-${{ matrix.arch }}
+      - volume=40gb
     name: "${{ matrix.arch }} | ${{ matrix.profile }} | ${{ matrix.shard }}"
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}

modules/nf-core/amulety/embed/environment.yml

@@ -6,9 +6,10 @@ channels:
 dependencies:
   - bioconda::igblast=1.22.0
   - conda-forge::curl=8.18.0
+  - conda-forge::pip=26.1.1
   - conda-forge::python=3.12.13
   - conda-forge::wget=1.25.0
   - pip:
-      - amulety==2.1.2
+      - amulety==2.1.3
       - torch==2.10.0
       - transformers==4.49.0

modules/nf-core/amulety/embed/main.nf

@@ -5,8 +5,8 @@ process AMULETY_EMBED {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ee/eef2fbc7c8d1ba71b3890a83b520c3eefa136ec4de5a8e6a97db828ae354d7ab/data':
-        'community.wave.seqera.io/library/igblast_curl_python_wget_pruned:07dda71433b05ed5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c3/c39fc87288811f7806452ecbdb559b9e9bba71aebb82c60d60af939a73bdf614/data':
+        'community.wave.seqera.io/library/igblast_curl_python_transformers_pruned:05685e2c81024d42' }"
 
     input:
     tuple val(meta), path(tsv)
@@ -17,6 +17,9 @@ process AMULETY_EMBED {
     tuple val(meta), path("${task.ext.prefix ?: meta.id}.tsv"), emit: embedding
     tuple val(meta), path("*metadata.tsv"), emit: embedding_metadata
     tuple val("${task.process}"), val('amulety'), eval("amulety --help 2>&1 | grep -o 'version [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'"), emit: versions_amulety, topic: versions
+    tuple val("${task.process}"), val('python'), eval("python --version 2>&1 | grep -o 'Python [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'"), emit: versions_python, topic: versions
+    tuple val("${task.process}"), val('pytorch'), eval("python -c 'import torch; print(torch.__version__)'"), emit: versions_pytorch, topic: versions
+    tuple val("${task.process}"), val('transformers'), eval("python -c 'import transformers; print(transformers.__version__)'"), emit: versions_transformers, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/amulety/embed/meta.yml

@@ -56,7 +56,7 @@ output:
           description: TSV with embeddings of BCR or TCR amino acid sequences.
           pattern: "*.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   embedding_metadata:
     - - meta:
           type: map
@@ -79,6 +79,36 @@ output:
       - amulety --help 2>&1 | grep -o 'version [0-9\.]\+' | grep -o '[0-9\.]\+':
           type: eval
           description: The command used to generate the version of the tool
+  versions_python:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The name of the tool
+      - python --version 2>&1 | grep -o 'Python [0-9\.]\+' | grep -o '[0-9\.]\+':
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_pytorch:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - pytorch:
+          type: string
+          description: The name of the tool
+      - python -c 'import torch; print(torch.__version__)':
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_transformers:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - transformers:
+          type: string
+          description: The name of the tool
+      - python -c 'import transformers; print(transformers.__version__)':
+          type: eval
+          description: The expression to obtain the version of the tool
 topics:
   versions:
     - - ${task.process}:
@@ -90,6 +120,33 @@ topics:
       - amulety --help 2>&1 | grep -o 'version [0-9\.]\+' | grep -o '[0-9\.]\+':
           type: eval
           description: The command used to generate the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The name of the tool
+      - python --version 2>&1 | grep -o 'Python [0-9\.]\+' | grep -o '[0-9\.]\+':
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - pytorch:
+          type: string
+          description: The name of the tool
+      - python -c 'import torch; print(torch.__version__)':
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - transformers:
+          type: string
+          description: The name of the tool
+      - python -c 'import transformers; print(transformers.__version__)':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@ggabernet"
 maintainers:

modules/nf-core/amulety/embed/tests/gpu.nf.test.snap

@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.tsv:md5,8ed0c1c7e8acc1bd8a5b3099c3cc0e53"
+                        "test.tsv:md5,1feb3fbc43aae1bb51d45e3552372240"
                     ]
                 ],
                 "1": [
@@ -24,7 +24,28 @@
                     [
                         "AMULETY_EMBED",
                         "amulety",
-                        "2.1.2"
+                        "2.1.3"
+                    ]
+                ],
+                "3": [
+                    [
+                        "AMULETY_EMBED",
+                        "python",
+                        "3.12.13"
+                    ]
+                ],
+                "4": [
+                    [
+                        "AMULETY_EMBED",
+                        "pytorch",
+                        "2.10.0+cu128"
+                    ]
+                ],
+                "5": [
+                    [
+                        "AMULETY_EMBED",
+                        "transformers",
+                        "4.49.0"
                     ]
                 ],
                 "embedding": [
@@ -33,7 +54,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.tsv:md5,8ed0c1c7e8acc1bd8a5b3099c3cc0e53"
+                        "test.tsv:md5,1feb3fbc43aae1bb51d45e3552372240"
                     ]
                 ],
                 "embedding_metadata": [
@@ -49,16 +70,37 @@
                     [
                         "AMULETY_EMBED",
                         "amulety",
-                        "2.1.2"
+                        "2.1.3"
+                    ]
+                ],
+                "versions_python": [
+                    [
+                        "AMULETY_EMBED",
+                        "python",
+                        "3.12.13"
+                    ]
+                ],
+                "versions_pytorch": [
+                    [
+                        "AMULETY_EMBED",
+                        "pytorch",
+                        "2.10.0+cu128"
+                    ]
+                ],
+                "versions_transformers": [
+                    [
+                        "AMULETY_EMBED",
+                        "transformers",
+                        "4.49.0"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-05-20T17:07:59.793052154",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-03-12T13:33:07.008006758"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
     },
     "human - AIRR rearrangement - stub": {
         "content": [
@@ -85,7 +127,28 @@
                     [
                         "AMULETY_EMBED",
                         "amulety",
-                        "2.1.2"
+                        "2.1.3"
+                    ]
+                ],
+                "3": [
+                    [
+                        "AMULETY_EMBED",
+                        "python",
+                        "3.12.13"
+                    ]
+                ],
+                "4": [
+                    [
+                        "AMULETY_EMBED",
+                        "pytorch",
+                        "2.10.0+cu128"
+                    ]
+                ],
+                "5": [
+                    [
+                        "AMULETY_EMBED",
+                        "transformers",
+                        "4.49.0"
                     ]
                 ],
                 "embedding": [
@@ -110,15 +173,36 @@
                     [
                         "AMULETY_EMBED",
                         "amulety",
-                        "2.1.2"
+                        "2.1.3"
+                    ]
+                ],
+                "versions_python": [
+                    [
+                        "AMULETY_EMBED",
+                        "python",
+                        "3.12.13"
+                    ]
+                ],
+                "versions_pytorch": [
+                    [
+                        "AMULETY_EMBED",
+                        "pytorch",
+                        "2.10.0+cu128"
+                    ]
+                ],
+                "versions_transformers": [
+                    [
+                        "AMULETY_EMBED",
+                        "transformers",
+                        "4.49.0"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-05-20T13:06:28.489036118",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-03-12T13:33:18.34555436"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
+        }
     }
 }