diff --git a/modules/nf-core/amulety/embed/environment.yml b/modules/nf-core/amulety/embed/environment.yml index 80cbdc85eac2..b9d52c282197 100644 --- a/modules/nf-core/amulety/embed/environment.yml +++ b/modules/nf-core/amulety/embed/environment.yml @@ -5,10 +5,10 @@ channels: - bioconda dependencies: - bioconda::igblast=1.22.0 - - conda-forge::curl=8.18.0 + - conda-forge::curl=8.20.0 - conda-forge::python=3.12.13 - conda-forge::wget=1.25.0 - pip: - - amulety==2.1.2 - - torch==2.10.0 + - amulety==2.1.3 + - torch==2.12.0 - transformers==4.49.0 diff --git a/modules/nf-core/amulety/embed/main.nf b/modules/nf-core/amulety/embed/main.nf index d7e279629e0d..75964757e659 100644 --- a/modules/nf-core/amulety/embed/main.nf +++ b/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/sha256/1a/1aefed63bbc301e069498001e90e26e8336c05aca6f5cef05c07e8cbda9eb179/data': + 'community.wave.seqera.io/library/igblast_curl_python_wget_pruned:d1590017ba067a17' }" input: tuple val(meta), path(tsv) diff --git a/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap b/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap index e5ec029a9d89..cb9107723aa2 100644 --- a/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap +++ b/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 +24,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ], "embedding": [ @@ -33,7 +33,7 @@ "id": "test", "single_end": false }, - "test.tsv:md5,8ed0c1c7e8acc1bd8a5b3099c3cc0e53" + "test.tsv:md5,1feb3fbc43aae1bb51d45e3552372240" ] ], "embedding_metadata": [ @@ -49,16 +49,16 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ] } ], + "timestamp": "2026-05-14T10:40:36.138512029", "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 +85,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ], "embedding": [ @@ -110,15 +110,15 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ] } ], + "timestamp": "2026-03-12T13:33:18.34555436", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-03-12T13:33:18.34555436" + } } } \ No newline at end of file diff --git a/modules/nf-core/amulety/embed/tests/main.nf.test.snap b/modules/nf-core/amulety/embed/tests/main.nf.test.snap index 5858ba9b8e85..70f779a0c0ea 100644 --- a/modules/nf-core/amulety/embed/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/main.nf.test.snap @@ -24,7 +24,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ], "embedding": [ @@ -49,16 +49,16 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ] } ], + "timestamp": "2026-05-14T10:41:03.994719942", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-03-12T13:33:37.430813005" + "nf-test": "0.9.5", + "nextflow": "26.04.1" + } }, "human - AIRR rearrangement - stub": { "content": [ @@ -85,7 +85,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ], "embedding": [ @@ -110,15 +110,15 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ] } ], + "timestamp": "2026-03-12T13:33:48.628764499", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-03-12T13:33:48.628764499" + } } } \ No newline at end of file diff --git a/modules/nf-core/amulety/translate/main.nf b/modules/nf-core/amulety/translate/main.nf index 67313b8ca8ea..27843ab4f0e7 100644 --- a/modules/nf-core/amulety/translate/main.nf +++ b/modules/nf-core/amulety/translate/main.nf @@ -4,8 +4,8 @@ process AMULETY_TRANSLATE { 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/sha256/1a/1aefed63bbc301e069498001e90e26e8336c05aca6f5cef05c07e8cbda9eb179/data': + 'community.wave.seqera.io/library/igblast_curl_python_wget_pruned:d1590017ba067a17' }" input: tuple val(meta), path(tsv) diff --git a/modules/nf-core/amulety/translate/tests/main.nf.test.snap b/modules/nf-core/amulety/translate/tests/main.nf.test.snap index c557683fdd2b..f8fde27e468f 100644 --- a/modules/nf-core/amulety/translate/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/translate/tests/main.nf.test.snap @@ -14,7 +14,7 @@ [ "AMULETY_TRANSLATE", "amulety", - "2.1.2" + "2.1.3" ] ], "2": [ @@ -36,7 +36,7 @@ [ "AMULETY_TRANSLATE", "amulety", - "2.1.2" + "2.1.3" ] ], "versions_igblastn": [ @@ -69,7 +69,7 @@ [ "AMULETY_TRANSLATE", "amulety", - "2.1.2" + "2.1.3" ] ], "2": [ @@ -91,7 +91,7 @@ [ "AMULETY_TRANSLATE", "amulety", - "2.1.2" + "2.1.3" ] ], "versions_igblastn": [