From df9b2e2bd3dbca7ab4bb3f5f095641df5231876e Mon Sep 17 00:00:00 2001
From: Gisela Gabernet <gisela.gabernet@gmail.com>
Date: Mon, 26 Jan 2026 13:28:18 -0500
Subject: [PATCH 01/14] 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 <gisela.gabernet@gmail.com>
Date: Mon, 26 Jan 2026 14:33:26 -0500
Subject: [PATCH 02/14] 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 <gisela.gabernet@gmail.com>
Date: Thu, 29 Jan 2026 13:43:21 -0500
Subject: [PATCH 03/14] 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 <gisela.gabernet@gmail.com>
Date: Thu, 29 Jan 2026 14:26:18 -0500
Subject: [PATCH 04/14] 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 <gisela.gabernet@gmail.com>
Date: Tue, 10 Mar 2026 11:01:57 -0400
Subject: [PATCH 05/14] 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 <gisela.gabernet@gmail.com>
Date: Wed, 11 Mar 2026 13:24:57 -0400
Subject: [PATCH 06/14] 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 <gisela.gabernet@gmail.com>
Date: Wed, 11 Mar 2026 13:25:58 -0400
Subject: [PATCH 07/14] merge upstream


From a4a04fe9dd37f398f975e9c59544f89425b74bd5 Mon Sep 17 00:00:00 2001
From: Gisela Gabernet <gisela.gabernet@gmail.com>
Date: Wed, 11 Mar 2026 16:24:05 -0400
Subject: [PATCH 08/14] 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 <gisela.gabernet@gmail.com>
Date: Wed, 11 Mar 2026 16:26:31 -0400
Subject: [PATCH 09/14] 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 <gisela.gabernet@gmail.com>
Date: Thu, 12 Mar 2026 11:46:54 -0400
Subject: [PATCH 10/14] 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 <gisela.gabernet@gmail.com>
Date: Thu, 12 Mar 2026 14:20:38 -0400
Subject: [PATCH 11/14] 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 <gisela.gabernet@gmail.com>
Date: Thu, 14 May 2026 10:31:28 -0400
Subject: [PATCH 12/14] 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 <gisela.gabernet@gmail.com>
Date: Thu, 14 May 2026 11:10:05 -0400
Subject: [PATCH 13/14] 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 <gisela.gabernet@gmail.com>
Date: Thu, 14 May 2026 11:46:04 -0400
Subject: [PATCH 14/14] 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": [