From df9b2e2bd3dbca7ab4bb3f5f095641df5231876e Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 26 Jan 2026 13:28:18 -0500 Subject: [PATCH 01/27] update amulety version --- modules/nf-core/amulety/embed/environment.yml | 4 +++- modules/nf-core/amulety/embed/main.nf | 4 ++-- .../nf-core/amulety/embed/tests/gpu.nf.test.snap | 16 ++++++++-------- .../amulety/embed/tests/main.nf.test.snap | 16 ++++++++-------- .../nf-core/amulety/translate/environment.yml | 3 ++- modules/nf-core/amulety/translate/main.nf | 4 ++-- .../amulety/translate/tests/main.nf.test.snap | 12 ++++++------ 7 files changed, 31 insertions(+), 28 deletions(-) diff --git a/modules/nf-core/amulety/embed/environment.yml b/modules/nf-core/amulety/embed/environment.yml index ee93301454bf..6a58bbefb5ff 100644 --- a/modules/nf-core/amulety/embed/environment.yml +++ b/modules/nf-core/amulety/embed/environment.yml @@ -4,4 +4,6 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::amulety=2.1.1" + - "bioconda::amulety=2.1.2" + - "conda-forge::wget=1.25.0" + - "conda-forge::curl=8.18.0" diff --git a/modules/nf-core/amulety/embed/main.nf b/modules/nf-core/amulety/embed/main.nf index 3ff77ee533d7..84fd1e80c39d 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 == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/amulety_wget:6bee673d7a6a9753': - 'community.wave.seqera.io/library/amulety_wget:662e66d72e77dc3a' }" + 'oras://community.wave.seqera.io/library/amulety_curl_wget:7e9b99e37a280bac': + 'community.wave.seqera.io/library/amulety_curl_wget:1b7068eb7e2d4527' }" 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 f96aeed14a36..73192db5d7cf 100644 --- a/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap @@ -9,7 +9,7 @@ "single_end": false }, [ - "test.tsv:md5,e7075849af049d716c9e1e3b3cd6b2eb", + "test.tsv:md5,534cdd836a5904728f282f133a1d819a", "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" ] ] @@ -18,7 +18,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.1" + "2.1.2" ] ], "embedding": [ @@ -28,7 +28,7 @@ "single_end": false }, [ - "test.tsv:md5,e7075849af049d716c9e1e3b3cd6b2eb", + "test.tsv:md5,534cdd836a5904728f282f133a1d819a", "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" ] ] @@ -37,7 +37,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.1" + "2.1.2" ] ] } @@ -46,7 +46,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-15T15:02:00.418773393" + "timestamp": "2026-01-26T13:12:31.560290659" }, "human - AIRR rearrangement - stub": { "content": [ @@ -64,7 +64,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.1" + "2.1.2" ] ], "embedding": [ @@ -80,7 +80,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.1" + "2.1.2" ] ] } @@ -89,6 +89,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-15T15:02:11.973327717" + "timestamp": "2026-01-26T13:12:42.728711071" } } \ 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 9c7e5e537437..327951c8f6a4 100644 --- a/modules/nf-core/amulety/embed/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "single_end": false }, [ - "test.tsv:md5,8b955ff6a1f6d655bbdbd6c842f71a7d", + "test.tsv:md5,534cdd836a5904728f282f133a1d819a", "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" ] ] @@ -18,7 +18,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.1" + "2.1.2" ] ], "embedding": [ @@ -28,7 +28,7 @@ "single_end": false }, [ - "test.tsv:md5,8b955ff6a1f6d655bbdbd6c842f71a7d", + "test.tsv:md5,534cdd836a5904728f282f133a1d819a", "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" ] ] @@ -37,7 +37,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.1" + "2.1.2" ] ] } @@ -46,7 +46,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-15T15:02:31.166209813" + "timestamp": "2026-01-26T13:13:05.18763832" }, "human - AIRR rearrangement - stub": { "content": [ @@ -64,7 +64,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.1" + "2.1.2" ] ], "embedding": [ @@ -80,7 +80,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.1" + "2.1.2" ] ] } @@ -89,6 +89,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-15T15:02:42.670600805" + "timestamp": "2026-01-26T13:13:16.575023384" } } \ No newline at end of file diff --git a/modules/nf-core/amulety/translate/environment.yml b/modules/nf-core/amulety/translate/environment.yml index 212ec1a812cc..62ba159dc03e 100644 --- a/modules/nf-core/amulety/translate/environment.yml +++ b/modules/nf-core/amulety/translate/environment.yml @@ -4,5 +4,6 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::amulety=2.1.1" + - "bioconda::amulety=2.1.2" - "bioconda::igblast=1.22.0" + - "conda-forge::wget=1.25.0" diff --git a/modules/nf-core/amulety/translate/main.nf b/modules/nf-core/amulety/translate/main.nf index 15652528eeaf..76fcc8fa92c5 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 == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/amulety_igblast_wget:63680dbda079196f': - 'community.wave.seqera.io/library/amulety_igblast_wget:0cc8c96f93ce70c3' }" + 'oras://community.wave.seqera.io/library/amulety_igblast_wget:7020cde3b45925f9': + 'community.wave.seqera.io/library/amulety_igblast_wget:e477bc17f7c35e7c' }" 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 cd760ae5306f..5128b91988a9 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", - "2.1.1" + "2.1.2" ] ], "2": [ @@ -36,7 +36,7 @@ [ "AMULETY_TRANSLATE", "amulety", - "2.1.1" + "2.1.2" ] ], "versions_igblastn": [ @@ -52,7 +52,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-15T15:28:14.200854685" + "timestamp": "2026-01-26T13:22:13.945389213" }, "human - AIRR rearrangement - stub": { "content": [ @@ -69,7 +69,7 @@ [ "AMULETY_TRANSLATE", "amulety", - "2.1.1" + "2.1.2" ] ], "2": [ @@ -91,7 +91,7 @@ [ "AMULETY_TRANSLATE", "amulety", - "2.1.1" + "2.1.2" ] ], "versions_igblastn": [ @@ -107,6 +107,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-15T15:28:24.271202255" + "timestamp": "2026-01-26T13:22:24.069686589" } } \ No newline at end of file From 45ff2e1baed6723ef6a1ae0e0fa93f1e112bde13 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 26 Jan 2026 14:33:26 -0500 Subject: [PATCH 02/27] update snapshot --- modules/nf-core/amulety/embed/tests/gpu.nf.test.snap | 4 ++-- modules/nf-core/amulety/embed/tests/main.nf.test.snap | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) 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 73192db5d7cf..60dfae975656 100644 --- a/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap @@ -9,7 +9,7 @@ "single_end": false }, [ - "test.tsv:md5,534cdd836a5904728f282f133a1d819a", + "test.tsv:md5,e7075849af049d716c9e1e3b3cd6b2eb", "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" ] ] @@ -28,7 +28,7 @@ "single_end": false }, [ - "test.tsv:md5,534cdd836a5904728f282f133a1d819a", + "test.tsv:md5,e7075849af049d716c9e1e3b3cd6b2eb", "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" ] ] 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 327951c8f6a4..1c50f34a62c1 100644 --- a/modules/nf-core/amulety/embed/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "single_end": false }, [ - "test.tsv:md5,534cdd836a5904728f282f133a1d819a", + "test.tsv:md5,8b955ff6a1f6d655bbdbd6c842f71a7d", "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" ] ] @@ -28,7 +28,7 @@ "single_end": false }, [ - "test.tsv:md5,534cdd836a5904728f282f133a1d819a", + "test.tsv:md5,8b955ff6a1f6d655bbdbd6c842f71a7d", "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" ] ] From 29b1939655eb4b2e600383b4d6b99e1bea0c2d7a Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 29 Jan 2026 13:43:21 -0500 Subject: [PATCH 03/27] update singularity oras to https --- modules/nf-core/amulety/embed/main.nf | 2 +- modules/nf-core/amulety/translate/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/amulety/embed/main.nf b/modules/nf-core/amulety/embed/main.nf index 84fd1e80c39d..4348df8164a2 100644 --- a/modules/nf-core/amulety/embed/main.nf +++ b/modules/nf-core/amulety/embed/main.nf @@ -5,7 +5,7 @@ process AMULETY_EMBED { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/amulety_curl_wget:7e9b99e37a280bac': + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bdc2f42370e0aa9a3f0b2a50ad4c613d07a76d2923cc4d2741b1a64a2cca552b/data': 'community.wave.seqera.io/library/amulety_curl_wget:1b7068eb7e2d4527' }" input: diff --git a/modules/nf-core/amulety/translate/main.nf b/modules/nf-core/amulety/translate/main.nf index 76fcc8fa92c5..71ea8449e378 100644 --- a/modules/nf-core/amulety/translate/main.nf +++ b/modules/nf-core/amulety/translate/main.nf @@ -4,7 +4,7 @@ process AMULETY_TRANSLATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/amulety_igblast_wget:7020cde3b45925f9': + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bdc2f42370e0aa9a3f0b2a50ad4c613d07a76d2923cc4d2741b1a64a2cca552b/data': 'community.wave.seqera.io/library/amulety_igblast_wget:e477bc17f7c35e7c' }" input: From 3479af5d71a93d83e66e1d983ef16d2e30ed2a7e Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 29 Jan 2026 14:26:18 -0500 Subject: [PATCH 04/27] update container --- modules/nf-core/amulety/translate/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/amulety/translate/main.nf b/modules/nf-core/amulety/translate/main.nf index 71ea8449e378..9692279b4fbe 100644 --- a/modules/nf-core/amulety/translate/main.nf +++ b/modules/nf-core/amulety/translate/main.nf @@ -4,7 +4,7 @@ process AMULETY_TRANSLATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bdc2f42370e0aa9a3f0b2a50ad4c613d07a76d2923cc4d2741b1a64a2cca552b/data': + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/53/53bd60c3aa7a937df11e4a3cbf66a274edd1d580aac1ef49a0c8d96d13d1f1fa/data': 'community.wave.seqera.io/library/amulety_igblast_wget:e477bc17f7c35e7c' }" input: From 8eceb3c03eba57d5276224eb91b193769d86b349 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 10 Mar 2026 11:01:57 -0400 Subject: [PATCH 05/27] fix amulety GPU support --- modules/nf-core/amulety/embed/main.nf | 4 +--- modules/nf-core/amulety/translate/main.nf | 3 ++- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/amulety/embed/main.nf b/modules/nf-core/amulety/embed/main.nf index 4348df8164a2..a09c7a6ae7c9 100644 --- a/modules/nf-core/amulety/embed/main.nf +++ b/modules/nf-core/amulety/embed/main.nf @@ -4,9 +4,7 @@ process AMULETY_EMBED { label 'process_gpu' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bdc2f42370e0aa9a3f0b2a50ad4c613d07a76d2923cc4d2741b1a64a2cca552b/data': - 'community.wave.seqera.io/library/amulety_curl_wget:1b7068eb7e2d4527' }" + container "docker.io/immcantation/amulety:2.1.2" // Seqera containers cannot be used since GPU is needed at runtime for pytorch with CUDA support to be installed input: tuple val(meta), path(tsv) diff --git a/modules/nf-core/amulety/translate/main.nf b/modules/nf-core/amulety/translate/main.nf index 9692279b4fbe..e01205bdc3f8 100644 --- a/modules/nf-core/amulety/translate/main.nf +++ b/modules/nf-core/amulety/translate/main.nf @@ -4,7 +4,7 @@ process AMULETY_TRANSLATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/53/53bd60c3aa7a937df11e4a3cbf66a274edd1d580aac1ef49a0c8d96d13d1f1fa/data': + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/88/88db7c962bd369a7886f2aeafb01a83e29092e4447365e7d00cea4f0a8971794/data': 'community.wave.seqera.io/library/amulety_igblast_wget:e477bc17f7c35e7c' }" input: @@ -26,6 +26,7 @@ process AMULETY_TRANSLATE { export IGDATA=${reference_igblast} amulety \\ translate-igblast \\ + --nproc ${task.cpus} \\ $args \\ --input-file $tsv \\ --output-dir . \\ From a7b78725f82d22cc0c5812214231d05d5bc56f8a Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 11 Mar 2026 13:24:57 -0400 Subject: [PATCH 06/27] fix container GPU --- modules/nf-core/amulety/embed/environment.yml | 11 ++++++++--- modules/nf-core/amulety/embed/main.nf | 9 ++++++--- modules/nf-core/amulety/embed/meta.yml | 12 ++++++++++++ .../nf-core/amulety/embed/tests/main.nf.test.snap | 4 ++-- modules/nf-core/amulety/translate/environment.yml | 11 ++++++++--- modules/nf-core/amulety/translate/main.nf | 4 ++-- 6 files changed, 38 insertions(+), 13 deletions(-) diff --git a/modules/nf-core/amulety/embed/environment.yml b/modules/nf-core/amulety/embed/environment.yml index 6a58bbefb5ff..3b1d84756f60 100644 --- a/modules/nf-core/amulety/embed/environment.yml +++ b/modules/nf-core/amulety/embed/environment.yml @@ -4,6 +4,11 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::amulety=2.1.2" - - "conda-forge::wget=1.25.0" - - "conda-forge::curl=8.18.0" + - conda-forge::wget=1.25.0 + - conda-forge::curl=8.18.0 + - bioconda::igblast=1.22.0 + - conda-forge::python=3.12.13 + - pip: + - torch==2.10.0 + - transformers==4.49.0 + - amulety==2.1.2 diff --git a/modules/nf-core/amulety/embed/main.nf b/modules/nf-core/amulety/embed/main.nf index a09c7a6ae7c9..c9720fa09313 100644 --- a/modules/nf-core/amulety/embed/main.nf +++ b/modules/nf-core/amulety/embed/main.nf @@ -4,15 +4,18 @@ process AMULETY_EMBED { label 'process_gpu' conda "${moduleDir}/environment.yml" - container "docker.io/immcantation/amulety:2.1.2" // Seqera containers cannot be used since GPU is needed at runtime for pytorch with CUDA support to be installed - + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ee/eef2fbc7c8d1ba71b3890a83b520c3eefa136ec4de5a8e6a97db828ae354d7ab/data': + 'community.wave.seqera.io/library/igblast_curl_python_wget_pruned:07dda71433b05ed5' }" + input: tuple val(meta), path(tsv) val(chain) val(model) output: - tuple val(meta), path("*.tsv"), emit: embedding + tuple val(meta), path("${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 when: diff --git a/modules/nf-core/amulety/embed/meta.yml b/modules/nf-core/amulety/embed/meta.yml index 9a4b3e8fcd25..d4984fe15619 100644 --- a/modules/nf-core/amulety/embed/meta.yml +++ b/modules/nf-core/amulety/embed/meta.yml @@ -55,6 +55,18 @@ output: pattern: "*.tsv" ontologies: - edam: http://edamontology.org/format_3475 # TSV + embedding_metadata: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*metadata.tsv": + type: file + description: TSV with metadata about the embeddings. + pattern: "*metadata.tsv" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV versions_amulety: - - ${task.process}: type: string diff --git a/modules/nf-core/amulety/embed/tests/main.nf.test.snap b/modules/nf-core/amulety/embed/tests/main.nf.test.snap index 1c50f34a62c1..b2bfe5311c6c 100644 --- a/modules/nf-core/amulety/embed/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "single_end": false }, [ - "test.tsv:md5,8b955ff6a1f6d655bbdbd6c842f71a7d", + "test.tsv:md5,492465dd5d0c27405f49ea419ccadafa", "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" ] ] @@ -28,7 +28,7 @@ "single_end": false }, [ - "test.tsv:md5,8b955ff6a1f6d655bbdbd6c842f71a7d", + "test.tsv:md5,492465dd5d0c27405f49ea419ccadafa", "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" ] ] diff --git a/modules/nf-core/amulety/translate/environment.yml b/modules/nf-core/amulety/translate/environment.yml index 62ba159dc03e..3b1d84756f60 100644 --- a/modules/nf-core/amulety/translate/environment.yml +++ b/modules/nf-core/amulety/translate/environment.yml @@ -4,6 +4,11 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::amulety=2.1.2" - - "bioconda::igblast=1.22.0" - - "conda-forge::wget=1.25.0" + - conda-forge::wget=1.25.0 + - conda-forge::curl=8.18.0 + - bioconda::igblast=1.22.0 + - conda-forge::python=3.12.13 + - pip: + - torch==2.10.0 + - transformers==4.49.0 + - amulety==2.1.2 diff --git a/modules/nf-core/amulety/translate/main.nf b/modules/nf-core/amulety/translate/main.nf index e01205bdc3f8..339b3b06ee6a 100644 --- a/modules/nf-core/amulety/translate/main.nf +++ b/modules/nf-core/amulety/translate/main.nf @@ -4,8 +4,8 @@ process AMULETY_TRANSLATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/88/88db7c962bd369a7886f2aeafb01a83e29092e4447365e7d00cea4f0a8971794/data': - 'community.wave.seqera.io/library/amulety_igblast_wget:e477bc17f7c35e7c' }" + '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' }" input: tuple val(meta), path(tsv) From 3af04ec1427840a5cbe90f1590d3c1dd98866e00 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 11 Mar 2026 13:25:58 -0400 Subject: [PATCH 07/27] merge upstream From a4a04fe9dd37f398f975e9c59544f89425b74bd5 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 11 Mar 2026 16:24:05 -0400 Subject: [PATCH 08/27] fix meta --- modules/nf-core/amulety/embed/environment.yml | 6 ++--- modules/nf-core/amulety/embed/meta.yml | 26 ++++++++++--------- .../nf-core/amulety/translate/environment.yml | 6 ++--- 3 files changed, 20 insertions(+), 18 deletions(-) diff --git a/modules/nf-core/amulety/embed/environment.yml b/modules/nf-core/amulety/embed/environment.yml index 3b1d84756f60..6b4a788457ee 100644 --- a/modules/nf-core/amulety/embed/environment.yml +++ b/modules/nf-core/amulety/embed/environment.yml @@ -4,11 +4,11 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::wget=1.25.0 - - conda-forge::curl=8.18.0 - bioconda::igblast=1.22.0 + - conda-forge::curl=8.18.0 - conda-forge::python=3.12.13 + - conda-forge::wget=1.25.0 - pip: + - amulety==2.1.2 - torch==2.10.0 - transformers==4.49.0 - - amulety==2.1.2 diff --git a/modules/nf-core/amulety/embed/meta.yml b/modules/nf-core/amulety/embed/meta.yml index d4984fe15619..cf6a57629c17 100644 --- a/modules/nf-core/amulety/embed/meta.yml +++ b/modules/nf-core/amulety/embed/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "amulety_embed" description: A module to create embeddings of B-cell receptor (BCR) or T-cell receptor (TCR) amino acid sequences using amulety. @@ -16,9 +15,9 @@ tools: documentation: "https://amulety.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/immcantation/amulety" doi: "10.1101/2025.03.21.644583" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: "" - input: - - meta: type: map @@ -30,18 +29,21 @@ input: description: TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format pattern: "*.{tsv}" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 - chain: type: string description: | The chain to use for the embeddings. Can be either 'H' (high diversity chain: BCR heavy or TCR beta or delta), 'L' (low diversity chain: BCR light or TCR alpha or gamma) or 'HL'/'LH' (BCR heavy + light, and TCR alpha + beta or gamma + delta). - enum: ["L", "H", "HL", "LH"] + enum: + - "L" + - "H" + - "HL" + - "LH" - model: type: string description: | The embedding model to use. Options are detailed on the amulety documentation. - output: embedding: - - meta: @@ -49,7 +51,7 @@ output: description: | Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` - - "*.tsv": + - "${task.ext.prefix ?: meta.id}.tsv": type: file description: TSV with embeddings of BCR or TCR amino acid sequences. pattern: "*.tsv" @@ -66,7 +68,7 @@ output: description: TSV with metadata about the embeddings. pattern: "*metadata.tsv" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 versions_amulety: - - ${task.process}: type: string @@ -74,8 +76,8 @@ output: - amulety: type: string description: The tool name - - "amulety --help 2>&1 | grep -o 'version [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": - type: string + - 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 topics: versions: @@ -85,8 +87,8 @@ topics: - amulety: type: string description: The tool name - - "amulety --help 2>&1 | grep -o 'version [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": - type: string + - 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 authors: - "@ggabernet" diff --git a/modules/nf-core/amulety/translate/environment.yml b/modules/nf-core/amulety/translate/environment.yml index 3b1d84756f60..6b4a788457ee 100644 --- a/modules/nf-core/amulety/translate/environment.yml +++ b/modules/nf-core/amulety/translate/environment.yml @@ -4,11 +4,11 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::wget=1.25.0 - - conda-forge::curl=8.18.0 - bioconda::igblast=1.22.0 + - conda-forge::curl=8.18.0 - conda-forge::python=3.12.13 + - conda-forge::wget=1.25.0 - pip: + - amulety==2.1.2 - torch==2.10.0 - transformers==4.49.0 - - amulety==2.1.2 From 1a91ef65f7de67626e877a4168d33b06aaef3bcb Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 11 Mar 2026 16:26:31 -0400 Subject: [PATCH 09/27] fix linting --- modules/nf-core/amulety/embed/environment.yml | 6 +++--- modules/nf-core/amulety/embed/main.nf | 2 +- modules/nf-core/amulety/translate/environment.yml | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/modules/nf-core/amulety/embed/environment.yml b/modules/nf-core/amulety/embed/environment.yml index 6b4a788457ee..80cbdc85eac2 100644 --- a/modules/nf-core/amulety/embed/environment.yml +++ b/modules/nf-core/amulety/embed/environment.yml @@ -9,6 +9,6 @@ dependencies: - conda-forge::python=3.12.13 - conda-forge::wget=1.25.0 - pip: - - amulety==2.1.2 - - torch==2.10.0 - - transformers==4.49.0 + - amulety==2.1.2 + - torch==2.10.0 + - transformers==4.49.0 diff --git a/modules/nf-core/amulety/embed/main.nf b/modules/nf-core/amulety/embed/main.nf index c9720fa09313..62954ff30bfa 100644 --- a/modules/nf-core/amulety/embed/main.nf +++ b/modules/nf-core/amulety/embed/main.nf @@ -7,7 +7,7 @@ process AMULETY_EMBED { container "${ workflow.containerEngine == 'singularity' && !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' }" - + input: tuple val(meta), path(tsv) val(chain) diff --git a/modules/nf-core/amulety/translate/environment.yml b/modules/nf-core/amulety/translate/environment.yml index 6b4a788457ee..80cbdc85eac2 100644 --- a/modules/nf-core/amulety/translate/environment.yml +++ b/modules/nf-core/amulety/translate/environment.yml @@ -9,6 +9,6 @@ dependencies: - conda-forge::python=3.12.13 - conda-forge::wget=1.25.0 - pip: - - amulety==2.1.2 - - torch==2.10.0 - - transformers==4.49.0 + - amulety==2.1.2 + - torch==2.10.0 + - transformers==4.49.0 From 7e3436bb4fa622a7fcd72ba358aee0da02ba77ff Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 12 Mar 2026 11:46:54 -0400 Subject: [PATCH 10/27] update snapshots --- modules/nf-core/amulety/embed/main.nf | 1 + .../amulety/embed/tests/gpu.nf.test.snap | 66 +++++++++---------- .../amulety/embed/tests/main.nf.test.snap | 66 +++++++++---------- .../amulety/translate/tests/main.nf.test.snap | 4 +- 4 files changed, 67 insertions(+), 70 deletions(-) diff --git a/modules/nf-core/amulety/embed/main.nf b/modules/nf-core/amulety/embed/main.nf index 62954ff30bfa..3feeffd956d4 100644 --- a/modules/nf-core/amulety/embed/main.nf +++ b/modules/nf-core/amulety/embed/main.nf @@ -42,5 +42,6 @@ process AMULETY_EMBED { """ touch ${prefix}.tsv + touch ${prefix}_metadata.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 60dfae975656..2131d1b7c0ab 100644 --- a/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap @@ -8,13 +8,19 @@ "id": "test", "single_end": false }, - [ - "test.tsv:md5,e7075849af049d716c9e1e3b3cd6b2eb", - "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" - ] + "test.tsv:md5,8ed0c1c7e8acc1bd8a5b3099c3cc0e53" ] ], "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" + ] + ], + "2": [ [ "AMULETY_EMBED", "amulety", @@ -27,10 +33,16 @@ "id": "test", "single_end": false }, - [ - "test.tsv:md5,e7075849af049d716c9e1e3b3cd6b2eb", - "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" - ] + "test.tsv:md5,8ed0c1c7e8acc1bd8a5b3099c3cc0e53" + ] + ], + "embedding_metadata": [ + [ + { + "id": "test", + "single_end": false + }, + "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" ] ], "versions_amulety": [ @@ -46,42 +58,28 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T13:12:31.560290659" + "timestamp": "2026-03-11T16:44:30.256201167" }, "human - AIRR rearrangement - stub": { "content": [ { "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - [ - "AMULETY_EMBED", - "amulety", - "2.1.2" - ] + + ], + "2": [ + ], "embedding": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + + ], + "embedding_metadata": [ + ], "versions_amulety": [ - [ - "AMULETY_EMBED", - "amulety", - "2.1.2" - ] + ] } ], @@ -89,6 +87,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T13:12:42.728711071" + "timestamp": "2026-03-11T16:44:41.349289759" } } \ 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 b2bfe5311c6c..37bd7ce50653 100644 --- a/modules/nf-core/amulety/embed/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/main.nf.test.snap @@ -8,13 +8,19 @@ "id": "test", "single_end": false }, - [ - "test.tsv:md5,492465dd5d0c27405f49ea419ccadafa", - "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" - ] + "test.tsv:md5,8ed0c1c7e8acc1bd8a5b3099c3cc0e53" ] ], "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" + ] + ], + "2": [ [ "AMULETY_EMBED", "amulety", @@ -27,10 +33,16 @@ "id": "test", "single_end": false }, - [ - "test.tsv:md5,492465dd5d0c27405f49ea419ccadafa", - "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" - ] + "test.tsv:md5,8ed0c1c7e8acc1bd8a5b3099c3cc0e53" + ] + ], + "embedding_metadata": [ + [ + { + "id": "test", + "single_end": false + }, + "test_metadata.tsv:md5,233805ee6b8c5ba151b1d864b2d02f4f" ] ], "versions_amulety": [ @@ -46,42 +58,28 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T13:13:05.18763832" + "timestamp": "2026-03-11T16:45:00.970648197" }, "human - AIRR rearrangement - stub": { "content": [ { "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - [ - "AMULETY_EMBED", - "amulety", - "2.1.2" - ] + + ], + "2": [ + ], "embedding": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + + ], + "embedding_metadata": [ + ], "versions_amulety": [ - [ - "AMULETY_EMBED", - "amulety", - "2.1.2" - ] + ] } ], @@ -89,6 +87,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T13:13:16.575023384" + "timestamp": "2026-03-11T16:45:12.013784846" } } \ No newline at end of file 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 5128b91988a9..c557683fdd2b 100644 --- a/modules/nf-core/amulety/translate/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/translate/tests/main.nf.test.snap @@ -52,7 +52,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T13:22:13.945389213" + "timestamp": "2026-03-11T20:50:20.544305034" }, "human - AIRR rearrangement - stub": { "content": [ @@ -107,6 +107,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T13:22:24.069686589" + "timestamp": "2026-03-11T20:50:30.828111924" } } \ No newline at end of file From 40dc8088247c3c636c05d5e3a10e429251cc66eb Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 12 Mar 2026 14:20:38 -0400 Subject: [PATCH 11/27] update stub snapshot --- .../amulety/embed/tests/gpu.nf.test.snap | 48 +++++++++++++++---- .../amulety/embed/tests/main.nf.test.snap | 48 +++++++++++++++---- 2 files changed, 80 insertions(+), 16 deletions(-) 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 2131d1b7c0ab..e5ec029a9d89 100644 --- a/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap @@ -58,28 +58,60 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-03-11T16:44:30.256201167" + "timestamp": "2026-03-12T13:33:07.008006758" }, "human - AIRR rearrangement - stub": { "content": [ { "0": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "1": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ - + [ + "AMULETY_EMBED", + "amulety", + "2.1.2" + ] ], "embedding": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "embedding_metadata": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions_amulety": [ - + [ + "AMULETY_EMBED", + "amulety", + "2.1.2" + ] ] } ], @@ -87,6 +119,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-03-11T16:44:41.349289759" + "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 37bd7ce50653..5858ba9b8e85 100644 --- a/modules/nf-core/amulety/embed/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/main.nf.test.snap @@ -58,28 +58,60 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-03-11T16:45:00.970648197" + "timestamp": "2026-03-12T13:33:37.430813005" }, "human - AIRR rearrangement - stub": { "content": [ { "0": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "1": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ - + [ + "AMULETY_EMBED", + "amulety", + "2.1.2" + ] ], "embedding": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "embedding_metadata": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions_amulety": [ - + [ + "AMULETY_EMBED", + "amulety", + "2.1.2" + ] ] } ], @@ -87,6 +119,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-03-11T16:45:12.013784846" + "timestamp": "2026-03-12T13:33:48.628764499" } } \ No newline at end of file From 2a43fb6eb1770f863b644cc8d2331e7306ed5dea Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 14 May 2026 10:31:28 -0400 Subject: [PATCH 12/27] update amulety version --- modules/nf-core/amulety/embed/environment.yml | 6 +++--- modules/nf-core/amulety/embed/main.nf | 4 ++-- modules/nf-core/amulety/embed/tests/gpu.nf.test.snap | 8 ++++---- modules/nf-core/amulety/embed/tests/main.nf.test.snap | 8 ++++---- modules/nf-core/amulety/translate/main.nf | 4 ++-- modules/nf-core/amulety/translate/tests/main.nf.test.snap | 8 ++++---- 6 files changed, 19 insertions(+), 19 deletions(-) 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..13a35b12cd83 100644 --- a/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap @@ -24,7 +24,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ], "embedding": [ @@ -49,7 +49,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ] } @@ -85,7 +85,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ], "embedding": [ @@ -110,7 +110,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ] } 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..0092aca36e8f 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": [ @@ -49,7 +49,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ] } @@ -85,7 +85,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ], "embedding": [ @@ -110,7 +110,7 @@ [ "AMULETY_EMBED", "amulety", - "2.1.2" + "2.1.3" ] ] } 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": [ From 193c0ad9672441ee4804890183169bbcc5f71c02 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 14 May 2026 11:10:05 -0400 Subject: [PATCH 13/27] update snapshot --- modules/nf-core/amulety/embed/tests/gpu.nf.test.snap | 12 ++++++------ .../nf-core/amulety/embed/tests/main.nf.test.snap | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) 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 13a35b12cd83..b892c56d8550 100644 --- a/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap @@ -54,11 +54,11 @@ ] } ], + "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": [ @@ -115,10 +115,10 @@ ] } ], + "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 0092aca36e8f..70f779a0c0ea 100644 --- a/modules/nf-core/amulety/embed/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/main.nf.test.snap @@ -54,11 +54,11 @@ ] } ], + "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": [ @@ -115,10 +115,10 @@ ] } ], + "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 From dd900a0c9b226ba6eb3ec28a95c9e156ef415949 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 14 May 2026 11:46:04 -0400 Subject: [PATCH 14/27] update gpu snapshot --- modules/nf-core/amulety/embed/tests/gpu.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 b892c56d8550..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": [ @@ -33,7 +33,7 @@ "id": "test", "single_end": false }, - "test.tsv:md5,8ed0c1c7e8acc1bd8a5b3099c3cc0e53" + "test.tsv:md5,1feb3fbc43aae1bb51d45e3552372240" ] ], "embedding_metadata": [ From 51c80a649997ad57aa32f2e7ee431b36a0807a59 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 18 May 2026 11:45:32 -0400 Subject: [PATCH 15/27] address review comments --- modules/nf-core/amulety/embed/environment.yml | 1 + modules/nf-core/amulety/embed/main.nf | 3 + .../amulety/embed/tests/gpu.nf.test.snap | 92 +++++++++++++++- .../amulety/embed/tests/main.nf.test.snap | 92 +++++++++++++++- .../nf-core/amulety/translate/environment.yml | 1 + modules/nf-core/amulety/translate/main.nf | 3 + .../amulety/translate/tests/main.nf.test.snap | 100 ++++++++++++++++-- 7 files changed, 276 insertions(+), 16 deletions(-) diff --git a/modules/nf-core/amulety/embed/environment.yml b/modules/nf-core/amulety/embed/environment.yml index b9d52c282197..2910c59bedfc 100644 --- a/modules/nf-core/amulety/embed/environment.yml +++ b/modules/nf-core/amulety/embed/environment.yml @@ -8,6 +8,7 @@ dependencies: - conda-forge::curl=8.20.0 - conda-forge::python=3.12.13 - conda-forge::wget=1.25.0 + - conda-forge::pip=26.1.1 - pip: - amulety==2.1.3 - torch==2.12.0 diff --git a/modules/nf-core/amulety/embed/main.nf b/modules/nf-core/amulety/embed/main.nf index 75964757e659..1bd3acc347e6 100644 --- a/modules/nf-core/amulety/embed/main.nf +++ b/modules/nf-core/amulety/embed/main.nf @@ -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 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 cb9107723aa2..bc9a4375ec43 100644 --- a/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap @@ -27,6 +27,27 @@ "2.1.3" ] ], + "3": [ + [ + "AMULETY_EMBED", + "python", + "3.12.13" + ] + ], + "4": [ + [ + "AMULETY_EMBED", + "pytorch", + "2.12.0+cu130" + ] + ], + "5": [ + [ + "AMULETY_EMBED", + "transformers", + "4.49.0" + ] + ], "embedding": [ [ { @@ -51,10 +72,31 @@ "amulety", "2.1.3" ] + ], + "versions_python": [ + [ + "AMULETY_EMBED", + "python", + "3.12.13" + ] + ], + "versions_pytorch": [ + [ + "AMULETY_EMBED", + "pytorch", + "2.12.0+cu130" + ] + ], + "versions_transformers": [ + [ + "AMULETY_EMBED", + "transformers", + "4.49.0" + ] ] } ], - "timestamp": "2026-05-14T10:40:36.138512029", + "timestamp": "2026-05-18T11:04:17.729964131", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.1" @@ -88,6 +130,27 @@ "2.1.3" ] ], + "3": [ + [ + "AMULETY_EMBED", + "python", + "3.12.13" + ] + ], + "4": [ + [ + "AMULETY_EMBED", + "pytorch", + "2.12.0+cu130" + ] + ], + "5": [ + [ + "AMULETY_EMBED", + "transformers", + "4.49.0" + ] + ], "embedding": [ [ { @@ -112,13 +175,34 @@ "amulety", "2.1.3" ] + ], + "versions_python": [ + [ + "AMULETY_EMBED", + "python", + "3.12.13" + ] + ], + "versions_pytorch": [ + [ + "AMULETY_EMBED", + "pytorch", + "2.12.0+cu130" + ] + ], + "versions_transformers": [ + [ + "AMULETY_EMBED", + "transformers", + "4.49.0" + ] ] } ], - "timestamp": "2026-03-12T13:33:18.34555436", + "timestamp": "2026-05-18T11:04:33.218055731", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nf-test": "0.9.5", + "nextflow": "26.04.1" } } } \ 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 70f779a0c0ea..aaefe9edc4aa 100644 --- a/modules/nf-core/amulety/embed/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/main.nf.test.snap @@ -27,6 +27,27 @@ "2.1.3" ] ], + "3": [ + [ + "AMULETY_EMBED", + "python", + "3.12.13" + ] + ], + "4": [ + [ + "AMULETY_EMBED", + "pytorch", + "2.12.0+cu130" + ] + ], + "5": [ + [ + "AMULETY_EMBED", + "transformers", + "4.49.0" + ] + ], "embedding": [ [ { @@ -51,10 +72,31 @@ "amulety", "2.1.3" ] + ], + "versions_python": [ + [ + "AMULETY_EMBED", + "python", + "3.12.13" + ] + ], + "versions_pytorch": [ + [ + "AMULETY_EMBED", + "pytorch", + "2.12.0+cu130" + ] + ], + "versions_transformers": [ + [ + "AMULETY_EMBED", + "transformers", + "4.49.0" + ] ] } ], - "timestamp": "2026-05-14T10:41:03.994719942", + "timestamp": "2026-05-18T11:04:58.086751748", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.1" @@ -88,6 +130,27 @@ "2.1.3" ] ], + "3": [ + [ + "AMULETY_EMBED", + "python", + "3.12.13" + ] + ], + "4": [ + [ + "AMULETY_EMBED", + "pytorch", + "2.12.0+cu130" + ] + ], + "5": [ + [ + "AMULETY_EMBED", + "transformers", + "4.49.0" + ] + ], "embedding": [ [ { @@ -112,13 +175,34 @@ "amulety", "2.1.3" ] + ], + "versions_python": [ + [ + "AMULETY_EMBED", + "python", + "3.12.13" + ] + ], + "versions_pytorch": [ + [ + "AMULETY_EMBED", + "pytorch", + "2.12.0+cu130" + ] + ], + "versions_transformers": [ + [ + "AMULETY_EMBED", + "transformers", + "4.49.0" + ] ] } ], - "timestamp": "2026-03-12T13:33:48.628764499", + "timestamp": "2026-05-18T11:05:13.058600505", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nf-test": "0.9.5", + "nextflow": "26.04.1" } } } \ No newline at end of file diff --git a/modules/nf-core/amulety/translate/environment.yml b/modules/nf-core/amulety/translate/environment.yml index 80cbdc85eac2..66b4111fdfa8 100644 --- a/modules/nf-core/amulety/translate/environment.yml +++ b/modules/nf-core/amulety/translate/environment.yml @@ -8,6 +8,7 @@ dependencies: - conda-forge::curl=8.18.0 - conda-forge::python=3.12.13 - conda-forge::wget=1.25.0 + - conda-forge::pip=26.1.1 - pip: - amulety==2.1.2 - torch==2.10.0 diff --git a/modules/nf-core/amulety/translate/main.nf b/modules/nf-core/amulety/translate/main.nf index 27843ab4f0e7..779e68cc20fe 100644 --- a/modules/nf-core/amulety/translate/main.nf +++ b/modules/nf-core/amulety/translate/main.nf @@ -15,6 +15,9 @@ process AMULETY_TRANSLATE { tuple val(meta), path("*_translated.tsv"), emit: repertoire_translated 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('igblastn'), eval("igblastn -version | grep -o 'igblast[0-9\\. ]\\+' | grep -o '[0-9\\. ]\\+'"), emit: versions_igblastn, 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 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 f8fde27e468f..8faece050c47 100644 --- a/modules/nf-core/amulety/translate/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/translate/tests/main.nf.test.snap @@ -24,6 +24,27 @@ " 1.22.0" ] ], + "3": [ + [ + "AMULETY_TRANSLATE", + "python", + "3.12.13" + ] + ], + "4": [ + [ + "AMULETY_TRANSLATE", + "pytorch", + "2.12.0+cu130" + ] + ], + "5": [ + [ + "AMULETY_TRANSLATE", + "transformers", + "4.49.0" + ] + ], "repertoire_translated": [ [ { @@ -45,14 +66,35 @@ "igblastn", " 1.22.0" ] + ], + "versions_python": [ + [ + "AMULETY_TRANSLATE", + "python", + "3.12.13" + ] + ], + "versions_pytorch": [ + [ + "AMULETY_TRANSLATE", + "pytorch", + "2.12.0+cu130" + ] + ], + "versions_transformers": [ + [ + "AMULETY_TRANSLATE", + "transformers", + "4.49.0" + ] ] } ], + "timestamp": "2026-05-18T11:06:19.501826162", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-03-11T20:50:20.544305034" + "nf-test": "0.9.5", + "nextflow": "26.04.1" + } }, "human - AIRR rearrangement - stub": { "content": [ @@ -79,6 +121,27 @@ " 1.22.0" ] ], + "3": [ + [ + "AMULETY_TRANSLATE", + "python", + "3.12.13" + ] + ], + "4": [ + [ + "AMULETY_TRANSLATE", + "pytorch", + "2.12.0+cu130" + ] + ], + "5": [ + [ + "AMULETY_TRANSLATE", + "transformers", + "4.49.0" + ] + ], "repertoire_translated": [ [ { @@ -100,13 +163,34 @@ "igblastn", " 1.22.0" ] + ], + "versions_python": [ + [ + "AMULETY_TRANSLATE", + "python", + "3.12.13" + ] + ], + "versions_pytorch": [ + [ + "AMULETY_TRANSLATE", + "pytorch", + "2.12.0+cu130" + ] + ], + "versions_transformers": [ + [ + "AMULETY_TRANSLATE", + "transformers", + "4.49.0" + ] ] } ], + "timestamp": "2026-05-18T11:06:30.783540244", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-03-11T20:50:30.828111924" + "nf-test": "0.9.5", + "nextflow": "26.04.1" + } } } \ No newline at end of file From 717c2cf5337d071515088dfe85a82f99f3b5ad87 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 19 May 2026 14:36:08 -0400 Subject: [PATCH 16/27] fix linting --- modules/nf-core/amulety/embed/environment.yml | 8 +- modules/nf-core/amulety/embed/meta.yml | 59 +++++++++++- .../nf-core/amulety/translate/environment.yml | 8 +- modules/nf-core/amulety/translate/meta.yml | 89 +++++++++++++++---- 4 files changed, 137 insertions(+), 27 deletions(-) diff --git a/modules/nf-core/amulety/embed/environment.yml b/modules/nf-core/amulety/embed/environment.yml index 2910c59bedfc..7b92500a77c6 100644 --- a/modules/nf-core/amulety/embed/environment.yml +++ b/modules/nf-core/amulety/embed/environment.yml @@ -6,10 +6,10 @@ channels: dependencies: - bioconda::igblast=1.22.0 - conda-forge::curl=8.20.0 + - conda-forge::pip=26.1.1 - conda-forge::python=3.12.13 - conda-forge::wget=1.25.0 - - conda-forge::pip=26.1.1 - pip: - - amulety==2.1.3 - - torch==2.12.0 - - transformers==4.49.0 + - amulety==2.1.3 + - torch==2.12.0 + - transformers==4.49.0 diff --git a/modules/nf-core/amulety/embed/meta.yml b/modules/nf-core/amulety/embed/meta.yml index cf6a57629c17..b6e6133f6119 100644 --- a/modules/nf-core/amulety/embed/meta.yml +++ b/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: diff --git a/modules/nf-core/amulety/translate/environment.yml b/modules/nf-core/amulety/translate/environment.yml index 66b4111fdfa8..2cb0b56c26c7 100644 --- a/modules/nf-core/amulety/translate/environment.yml +++ b/modules/nf-core/amulety/translate/environment.yml @@ -6,10 +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 - - conda-forge::pip=26.1.1 - pip: - - amulety==2.1.2 - - torch==2.10.0 - - transformers==4.49.0 + - amulety==2.1.2 + - torch==2.10.0 + - transformers==4.49.0 diff --git a/modules/nf-core/amulety/translate/meta.yml b/modules/nf-core/amulety/translate/meta.yml index b674141ae37b..9b2d5f421bb7 100644 --- a/modules/nf-core/amulety/translate/meta.yml +++ b/modules/nf-core/amulety/translate/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "amulety_translate" description: A module to translate BCR and TCR nucleotide sequences into amino acid sequences using amulety and igblast. @@ -17,7 +16,8 @@ tools: documentation: "https://amulety.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/immcantation/amulety" doi: "10.1101/2025.03.21.644583" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: "" - "igblast": description: "A tool for immunoglobulin (IG, BCR) and T cell receptor (TCR) V @@ -26,9 +26,9 @@ tools: documentation: "https://ncbi.github.io/igblast/" tool_dev_url: "https://github.com/ncbi/igblast" doi: "10.1093/nar/gkt382" - licence: ["United States Government Work"] + licence: + - "United States Government Work" identifier: biotools:igblast - input: - - meta: type: map @@ -40,11 +40,10 @@ input: description: TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format pattern: "*.{tsv}" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 - reference_igblast: type: file description: Built reference databases for igblast - ontologies: [] output: repertoire_translated: @@ -57,9 +56,8 @@ output: type: file description: TSV with BCR/TCR amino acid sequences in AIRR rearrangement format pattern: "*.tsv" - ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 versions_amulety: - - ${task.process}: type: string @@ -67,8 +65,8 @@ output: - amulety: type: string description: The tool name - - "amulety --help 2>&1 | grep -o 'version [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": - type: string + - 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_igblastn: - - ${task.process}: @@ -77,10 +75,39 @@ output: - igblastn: type: string description: The tool name - - "igblastn -version | grep -o 'igblast[0-9\\. ]\\+' | grep -o '[0-9\\. ]\\+'": - type: string + - igblastn -version | grep -o 'igblast[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}: @@ -89,8 +116,8 @@ topics: - amulety: type: string description: The tool name - - "amulety --help 2>&1 | grep -o 'version [0-9\\.]\\+' | grep -o '[0-9\\.]\\+'": - type: string + - 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 @@ -98,10 +125,36 @@ topics: - igblastn: type: string description: The tool name - - "igblastn -version | grep -o 'igblast[0-9\\. ]\\+' | grep -o '[0-9\\. ]\\+'": - type: string + - igblastn -version | grep -o 'igblast[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 + - - ${task.process}: + type: string + description: The process the versions were collected from + - transformers: + type: string + description: The name of the tool + - python -c 'import transformers; print(transformers.__version__)': + type: eval + description: The expression to obtain the version of the tool authors: - "@ggabernet" maintainers: From a4df03ef050a19114bb8f7c19c876a4109fad827 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 19 May 2026 15:02:46 -0400 Subject: [PATCH 17/27] test increase CI volume --- .github/workflows/nf-test-gpu.yml | 1 + .github/workflows/nf-test.yml | 1 + 2 files changed, 2 insertions(+) diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml index 31baa52cda84..2a8e35784d0e 100644 --- a/.github/workflows/nf-test-gpu.yml +++ b/.github/workflows/nf-test-gpu.yml @@ -38,6 +38,7 @@ jobs: runs-on: - runs-on=${{ github.run_id }}-nf-test-changes-gpu - runner=4cpu-linux-x64 + - volume=40gb - image=ubuntu22-full-x64 outputs: # gpu tag outputs diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 4d9a7a25c64f..8b10190a43b0 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -36,6 +36,7 @@ jobs: runs-on: - runs-on=${{ github.run_id }}-nf-test-changes - runner=4cpu-linux-x64 + - volume=40gb - image=ubuntu22-full-x64 outputs: # Expose detected tags as 'modules' and 'workflows' output variables From 5e27acb0b012e1bac7c81e81d9add128b6743bc9 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 19 May 2026 21:26:48 -0400 Subject: [PATCH 18/27] increase volume for nf-tests --- .github/workflows/nf-test-gpu.yml | 7 +++++-- .github/workflows/nf-test.yml | 2 +- modules/nf-core/amulety/embed/environment.yml | 6 +++--- modules/nf-core/amulety/translate/environment.yml | 6 +++--- 4 files changed, 12 insertions(+), 9 deletions(-) diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml index 2a8e35784d0e..13f2aab3a31e 100644 --- a/.github/workflows/nf-test-gpu.yml +++ b/.github/workflows/nf-test-gpu.yml @@ -38,7 +38,6 @@ jobs: runs-on: - runs-on=${{ github.run_id }}-nf-test-changes-gpu - runner=4cpu-linux-x64 - - volume=40gb - image=ubuntu22-full-x64 outputs: # gpu tag outputs @@ -105,7 +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: ${{ needs.nf-test-changes.outputs.gpu_total_shards != '0' && needs.nf-test-changes.outputs.gpu_total_shards != '' }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 8b10190a43b0..da2e4495936e 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -36,7 +36,6 @@ jobs: runs-on: - runs-on=${{ github.run_id }}-nf-test-changes - runner=4cpu-linux-x64 - - volume=40gb - image=ubuntu22-full-x64 outputs: # Expose detected tags as 'modules' and 'workflows' output variables @@ -94,6 +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' }} diff --git a/modules/nf-core/amulety/embed/environment.yml b/modules/nf-core/amulety/embed/environment.yml index 7b92500a77c6..e4a8f7c227ef 100644 --- a/modules/nf-core/amulety/embed/environment.yml +++ b/modules/nf-core/amulety/embed/environment.yml @@ -10,6 +10,6 @@ dependencies: - conda-forge::python=3.12.13 - conda-forge::wget=1.25.0 - pip: - - amulety==2.1.3 - - torch==2.12.0 - - transformers==4.49.0 + - amulety==2.1.3 + - torch==2.12.0 + - transformers==4.49.0 diff --git a/modules/nf-core/amulety/translate/environment.yml b/modules/nf-core/amulety/translate/environment.yml index 2cb0b56c26c7..bf388aec72fd 100644 --- a/modules/nf-core/amulety/translate/environment.yml +++ b/modules/nf-core/amulety/translate/environment.yml @@ -10,6 +10,6 @@ dependencies: - conda-forge::python=3.12.13 - conda-forge::wget=1.25.0 - pip: - - amulety==2.1.2 - - torch==2.10.0 - - transformers==4.49.0 + - amulety==2.1.2 + - torch==2.10.0 + - transformers==4.49.0 From 4beadcce2e3f1316e6395b643f0a8b154d87896d Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 19 May 2026 21:42:01 -0400 Subject: [PATCH 19/27] test pin down torch --- modules/nf-core/amulety/embed/environment.yml | 2 +- modules/nf-core/amulety/translate/environment.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/amulety/embed/environment.yml b/modules/nf-core/amulety/embed/environment.yml index e4a8f7c227ef..a70aae6f7830 100644 --- a/modules/nf-core/amulety/embed/environment.yml +++ b/modules/nf-core/amulety/embed/environment.yml @@ -11,5 +11,5 @@ dependencies: - conda-forge::wget=1.25.0 - pip: - amulety==2.1.3 - - torch==2.12.0 + - torch==2.10.0 - transformers==4.49.0 diff --git a/modules/nf-core/amulety/translate/environment.yml b/modules/nf-core/amulety/translate/environment.yml index bf388aec72fd..3bce418c6a17 100644 --- a/modules/nf-core/amulety/translate/environment.yml +++ b/modules/nf-core/amulety/translate/environment.yml @@ -10,6 +10,6 @@ dependencies: - 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 From 93f66b8440259d5b3352beb6eb2d8aa5afbfdfde Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 20 May 2026 10:55:10 -0400 Subject: [PATCH 20/27] fix env --- modules/nf-core/amulety/embed/environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/amulety/embed/environment.yml b/modules/nf-core/amulety/embed/environment.yml index a70aae6f7830..7e8061b70ea1 100644 --- a/modules/nf-core/amulety/embed/environment.yml +++ b/modules/nf-core/amulety/embed/environment.yml @@ -5,11 +5,11 @@ channels: - bioconda dependencies: - bioconda::igblast=1.22.0 - - conda-forge::curl=8.20.0 + - 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==2.1.3 - torch==2.10.0 - - transformers==4.49.0 + - transformers==4.49.0 \ No newline at end of file From 884d0dbab3e2a7c63b442ad10adabcc1dd4e7db7 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 20 May 2026 11:28:32 -0400 Subject: [PATCH 21/27] increase volume --- .github/workflows/nf-test-gpu.yml | 4 ++-- .github/workflows/nf-test.yml | 2 +- modules/nf-core/amulety/embed/environment.yml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml index 13f2aab3a31e..5ffd49d6068d 100644 --- a/.github/workflows/nf-test-gpu.yml +++ b/.github/workflows/nf-test-gpu.yml @@ -104,11 +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: - runs-on=${{ github.run_id }} - family=g4dn.xlarge - image=ubuntu24-gpu-x64 - - volume=40gb + - volume=50gb name: "GPU Test | g4dn.xlarge | ${{ matrix.profile }} | ${{ matrix.shard }}" needs: [nf-test-changes] if: ${{ needs.nf-test-changes.outputs.gpu_total_shards != '0' && needs.nf-test-changes.outputs.gpu_total_shards != '' }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index da2e4495936e..c5ac9dc76ae6 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -93,7 +93,7 @@ jobs: - runs-on=${{ github.run_id }} - runner=4cpu-linux-${{ matrix.arch }} - image=ubuntu24-full-${{ matrix.arch }} - - volume=40gb + - volume=50gb name: "${{ matrix.arch }} | ${{ matrix.profile }} | ${{ matrix.shard }}" needs: [nf-test-changes] if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} diff --git a/modules/nf-core/amulety/embed/environment.yml b/modules/nf-core/amulety/embed/environment.yml index 7e8061b70ea1..3bce418c6a17 100644 --- a/modules/nf-core/amulety/embed/environment.yml +++ b/modules/nf-core/amulety/embed/environment.yml @@ -12,4 +12,4 @@ dependencies: - pip: - amulety==2.1.3 - torch==2.10.0 - - transformers==4.49.0 \ No newline at end of file + - transformers==4.49.0 From 858ea5a672644f0810e45f9a1024e1f8528bed0e Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 20 May 2026 11:53:35 -0400 Subject: [PATCH 22/27] test increase volume --- .github/workflows/nf-test-gpu.yml | 2 +- .github/workflows/nf-test.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml index 5ffd49d6068d..a038eede9655 100644 --- a/.github/workflows/nf-test-gpu.yml +++ b/.github/workflows/nf-test-gpu.yml @@ -108,7 +108,7 @@ jobs: - runs-on=${{ github.run_id }} - family=g4dn.xlarge - image=ubuntu24-gpu-x64 - - volume=50gb + - volume=60gb name: "GPU Test | g4dn.xlarge | ${{ matrix.profile }} | ${{ matrix.shard }}" needs: [nf-test-changes] if: ${{ needs.nf-test-changes.outputs.gpu_total_shards != '0' && needs.nf-test-changes.outputs.gpu_total_shards != '' }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index c5ac9dc76ae6..a712892c2565 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -93,7 +93,7 @@ jobs: - runs-on=${{ github.run_id }} - runner=4cpu-linux-${{ matrix.arch }} - image=ubuntu24-full-${{ matrix.arch }} - - volume=50gb + - volume=60gb name: "${{ matrix.arch }} | ${{ matrix.profile }} | ${{ matrix.shard }}" needs: [nf-test-changes] if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} From 3cf3a8d9f9b11728291d134b2e43b89bf9d1a895 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 20 May 2026 11:55:27 -0400 Subject: [PATCH 23/27] set volume back --- .github/workflows/nf-test-gpu.yml | 2 +- .github/workflows/nf-test.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml index a038eede9655..5ffd49d6068d 100644 --- a/.github/workflows/nf-test-gpu.yml +++ b/.github/workflows/nf-test-gpu.yml @@ -108,7 +108,7 @@ jobs: - runs-on=${{ github.run_id }} - family=g4dn.xlarge - image=ubuntu24-gpu-x64 - - volume=60gb + - volume=50gb name: "GPU Test | g4dn.xlarge | ${{ matrix.profile }} | ${{ matrix.shard }}" needs: [nf-test-changes] if: ${{ needs.nf-test-changes.outputs.gpu_total_shards != '0' && needs.nf-test-changes.outputs.gpu_total_shards != '' }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index a712892c2565..c5ac9dc76ae6 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -93,7 +93,7 @@ jobs: - runs-on=${{ github.run_id }} - runner=4cpu-linux-${{ matrix.arch }} - image=ubuntu24-full-${{ matrix.arch }} - - volume=60gb + - volume=50gb name: "${{ matrix.arch }} | ${{ matrix.profile }} | ${{ matrix.shard }}" needs: [nf-test-changes] if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} From 6d5046237f5c08c54d2f3da03a1db18714a89496 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 20 May 2026 13:26:23 -0400 Subject: [PATCH 24/27] update torch version --- modules/nf-core/amulety/embed/main.nf | 4 ++-- modules/nf-core/amulety/embed/tests/gpu.nf.test.snap | 12 ++++++------ .../nf-core/amulety/embed/tests/main.nf.test.snap | 12 ++++++------ modules/nf-core/amulety/translate/main.nf | 4 ++-- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/modules/nf-core/amulety/embed/main.nf b/modules/nf-core/amulety/embed/main.nf index 1bd3acc347e6..078dfa002567 100644 --- a/modules/nf-core/amulety/embed/main.nf +++ b/modules/nf-core/amulety/embed/main.nf @@ -5,8 +5,8 @@ process AMULETY_EMBED { conda "${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/sha256/1a/1aefed63bbc301e069498001e90e26e8336c05aca6f5cef05c07e8cbda9eb179/data': - 'community.wave.seqera.io/library/igblast_curl_python_wget_pruned:d1590017ba067a17' }" + '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) 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 bc9a4375ec43..0b9b04bb068d 100644 --- a/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/gpu.nf.test.snap @@ -38,7 +38,7 @@ [ "AMULETY_EMBED", "pytorch", - "2.12.0+cu130" + "2.10.0+cu128" ] ], "5": [ @@ -84,7 +84,7 @@ [ "AMULETY_EMBED", "pytorch", - "2.12.0+cu130" + "2.10.0+cu128" ] ], "versions_transformers": [ @@ -96,7 +96,7 @@ ] } ], - "timestamp": "2026-05-18T11:04:17.729964131", + "timestamp": "2026-05-20T13:06:14.298139564", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.1" @@ -141,7 +141,7 @@ [ "AMULETY_EMBED", "pytorch", - "2.12.0+cu130" + "2.10.0+cu128" ] ], "5": [ @@ -187,7 +187,7 @@ [ "AMULETY_EMBED", "pytorch", - "2.12.0+cu130" + "2.10.0+cu128" ] ], "versions_transformers": [ @@ -199,7 +199,7 @@ ] } ], - "timestamp": "2026-05-18T11:04:33.218055731", + "timestamp": "2026-05-20T13:06:28.489036118", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.1" 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 aaefe9edc4aa..3c0842669d2f 100644 --- a/modules/nf-core/amulety/embed/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/main.nf.test.snap @@ -38,7 +38,7 @@ [ "AMULETY_EMBED", "pytorch", - "2.12.0+cu130" + "2.10.0+cu128" ] ], "5": [ @@ -84,7 +84,7 @@ [ "AMULETY_EMBED", "pytorch", - "2.12.0+cu130" + "2.10.0+cu128" ] ], "versions_transformers": [ @@ -96,7 +96,7 @@ ] } ], - "timestamp": "2026-05-18T11:04:58.086751748", + "timestamp": "2026-05-20T13:06:51.502387581", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.1" @@ -141,7 +141,7 @@ [ "AMULETY_EMBED", "pytorch", - "2.12.0+cu130" + "2.10.0+cu128" ] ], "5": [ @@ -187,7 +187,7 @@ [ "AMULETY_EMBED", "pytorch", - "2.12.0+cu130" + "2.10.0+cu128" ] ], "versions_transformers": [ @@ -199,7 +199,7 @@ ] } ], - "timestamp": "2026-05-18T11:05:13.058600505", + "timestamp": "2026-05-20T13:07:05.608365281", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.1" diff --git a/modules/nf-core/amulety/translate/main.nf b/modules/nf-core/amulety/translate/main.nf index 779e68cc20fe..f972027a4114 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/sha256/1a/1aefed63bbc301e069498001e90e26e8336c05aca6f5cef05c07e8cbda9eb179/data': - 'community.wave.seqera.io/library/igblast_curl_python_wget_pruned:d1590017ba067a17' }" + '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) From 4bb16ab72fd820ce15455a9b22586142d6bd4f88 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 20 May 2026 22:33:59 -0400 Subject: [PATCH 25/27] update cuda --- modules/nf-core/amulety/embed/tests/gpu.nf.test.snap | 6 +++--- .../nf-core/amulety/embed/tests/main.nf.test.snap | 2 +- .../amulety/translate/tests/main.nf.test.snap | 12 ++++++------ 3 files changed, 10 insertions(+), 10 deletions(-) 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 0b9b04bb068d..73f62274a93a 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:md5,1feb3fbc43aae1bb51d45e3552372240" + "test.tsv:md5,209a7b4b97ce65fd220e2016b009b5fc" ] ], "1": [ @@ -54,7 +54,7 @@ "id": "test", "single_end": false }, - "test.tsv:md5,1feb3fbc43aae1bb51d45e3552372240" + "test.tsv:md5,209a7b4b97ce65fd220e2016b009b5fc" ] ], "embedding_metadata": [ @@ -96,7 +96,7 @@ ] } ], - "timestamp": "2026-05-20T13:06:14.298139564", + "timestamp": "2026-05-20T17:07:59.793052154", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.1" 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 3c0842669d2f..262bb29bf823 100644 --- a/modules/nf-core/amulety/embed/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/embed/tests/main.nf.test.snap @@ -96,7 +96,7 @@ ] } ], - "timestamp": "2026-05-20T13:06:51.502387581", + "timestamp": "2026-05-20T17:08:38.75770715", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.1" 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 8faece050c47..d6f7237c321a 100644 --- a/modules/nf-core/amulety/translate/tests/main.nf.test.snap +++ b/modules/nf-core/amulety/translate/tests/main.nf.test.snap @@ -35,7 +35,7 @@ [ "AMULETY_TRANSLATE", "pytorch", - "2.12.0+cu130" + "2.10.0+cu128" ] ], "5": [ @@ -78,7 +78,7 @@ [ "AMULETY_TRANSLATE", "pytorch", - "2.12.0+cu130" + "2.10.0+cu128" ] ], "versions_transformers": [ @@ -90,7 +90,7 @@ ] } ], - "timestamp": "2026-05-18T11:06:19.501826162", + "timestamp": "2026-05-20T17:09:55.985085263", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.1" @@ -132,7 +132,7 @@ [ "AMULETY_TRANSLATE", "pytorch", - "2.12.0+cu130" + "2.10.0+cu128" ] ], "5": [ @@ -175,7 +175,7 @@ [ "AMULETY_TRANSLATE", "pytorch", - "2.12.0+cu130" + "2.10.0+cu128" ] ], "versions_transformers": [ @@ -187,7 +187,7 @@ ] } ], - "timestamp": "2026-05-18T11:06:30.783540244", + "timestamp": "2026-05-20T17:10:06.304029128", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.1" From b1d1e3fab480779b66cb4d8afb40a1f39fac56ec Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Wed, 20 May 2026 22:57:45 -0400 Subject: [PATCH 26/27] update checksums --- modules/nf-core/amulety/embed/tests/gpu.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 73f62274a93a..24da72f42f25 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:md5,209a7b4b97ce65fd220e2016b009b5fc" + "test.tsv:md5,1feb3fbc43aae1bb51d45e3552372240" ] ], "1": [ @@ -54,7 +54,7 @@ "id": "test", "single_end": false }, - "test.tsv:md5,209a7b4b97ce65fd220e2016b009b5fc" + "test.tsv:md5,1feb3fbc43aae1bb51d45e3552372240" ] ], "embedding_metadata": [ From 82eeb83e91c340dd88f3adf408f0fcbe6b390d2b Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Thu, 21 May 2026 11:18:05 -0400 Subject: [PATCH 27/27] reduce volume to 40GB default --- .github/workflows/nf-test-gpu.yml | 2 +- .github/workflows/nf-test.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml index 5ffd49d6068d..88768f2af9ad 100644 --- a/.github/workflows/nf-test-gpu.yml +++ b/.github/workflows/nf-test-gpu.yml @@ -108,7 +108,7 @@ jobs: - runs-on=${{ github.run_id }} - family=g4dn.xlarge - image=ubuntu24-gpu-x64 - - volume=50gb + - volume=40gb name: "GPU Test | g4dn.xlarge | ${{ matrix.profile }} | ${{ matrix.shard }}" needs: [nf-test-changes] if: ${{ needs.nf-test-changes.outputs.gpu_total_shards != '0' && needs.nf-test-changes.outputs.gpu_total_shards != '' }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index c5ac9dc76ae6..da2e4495936e 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -93,7 +93,7 @@ jobs: - runs-on=${{ github.run_id }} - runner=4cpu-linux-${{ matrix.arch }} - image=ubuntu24-full-${{ matrix.arch }} - - volume=50gb + - volume=40gb name: "${{ matrix.arch }} | ${{ matrix.profile }} | ${{ matrix.shard }}" needs: [nf-test-changes] if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}