diff --git a/modules/nf-core/amulety/antiberta2/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt b/modules/nf-core/amulety/antiberta2/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
new file mode 100644
index 000000000000..a667b571ba52
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+sha256: 59fe996e2d860ec2a30bb5f204c5c807735eb2fb7aa4ab491f79053de28a5b15
+md5: 8784f3a566787f27a705f304e8357aa1
+depends:
+- huggingface_hub >=0.16.4,<2.0
+- libgcc >=14
+- libstdcxx >=14
+- openssl >=3.5.4,<4.0a0
+- python >=3.14,<3.15.0a0
+- python >=3.14,<3.15.0a0 *_cp314
+- python_abi 3.14.* *_cp314
+constrains:
+- __glibc >=2.17
+license: Apache-2.0
+license_family: APACHE
+size: 2438359
+timestamp: 1764695098756
+- conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.4.1-pyhcf101f3_0.conda
+sha256: 91cafdb64268e43e0e10d30bd1bef5af392e69f00edd34dfaf909f69ab2da6bd
+md5: b5325cf06a000c5b14970462ff5e4d58
+depends:
+- python >=3.10
+- python
+license: MIT
+license_family: MIT
+size: 21561
+timestamp: 1774492402955
+- conda: https://conda.anaconda.org/conda-forge/noarch/tqdm-4.70.0-pyh8f84b5b_0.conda
+sha256: a4d9e9da15b13f1ab047e7db412e2ed564bc615832e80213cf129b973c3abf4a
+md5: 00953c3b729e03b0ae21f49fdf3441bb
+depends:
+- python >=3.10
+- __unix
+- python
+constrains:
+- envwrap >=0.2
+- ipywidgets >=6.0
+license: MPL-2.0 and MIT
+size: 98184
+timestamp: 1785172528905
+- conda: https://conda.anaconda.org/conda-forge/noarch/transformers-5.14.1-pyhcf101f3_0.conda
+sha256: aca27f98965064da34c0baa63c5d69cbe84fb85607b3c45af37f7e3ee6bf4c7e
+md5: e9a596eee896e0b5525054aaff759c3a
+depends:
+- python >=3.10
+- huggingface_hub >=1.5.0,<2.0
+- numpy >=1.17
+- packaging >=20.0
+- pyyaml >=5.1
+- regex >=2025.10.22
+- tokenizers >=0.22.0,<=0.23.0
+- typer
+- safetensors >=0.8.0
+- tqdm >=4.60
+- python
+license: Apache-2.0
+license_family: APACHE
+size: 4397095
+timestamp: 1784221007396
+- conda: https://conda.anaconda.org/conda-forge/noarch/typer-0.27.0-pyhcf101f3_0.conda
+sha256: f44984374b248c45f7e3d43a2cb0bf73d1441ecea07fb73198e89f643f6c5824
+md5: aa0ef00569728be93656de5f097fc81d
+depends:
+- annotated-doc >=0.0.2
+- colorama
+- python >=3.10
+- rich >=13.8.0
+- shellingham >=1.3.0
+- python
+license: MIT AND BSD-3-Clause
+size: 187450
+timestamp: 1784167351535
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.16.0-h69aa097_0.conda
+sha256: b141933ece3518f6d7b75dfb59451e2f26b405a44c18e2518a83e9a02e09315c
+md5: c680b5747e8c4c8f23dca0bb7042a8fc
+depends:
+- typing_extensions ==4.16.0 pyhcf101f3_0
+license: PSF-2.0
+license_family: PSF
+size: 94080
+timestamp: 1783002732887
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.16.0-pyhcf101f3_0.conda
+sha256: 2d888f90af0686044882c74193ec80a90ec1943145d94a7b1b048958acda1848
+md5: c70ad746c22219b9700931707482992c
+depends:
+- python >=3.10
+- python
+license: PSF-2.0
+license_family: PSF
+size: 52631
+timestamp: 1783002732887
+- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2026c-h151e31d_0.conda
+sha256: b928c30ddcb0e3f544c6eade8352737e6e610e263276b90232db6a578ef899d8
+md5: fcb489df604d100968b737f2cb6076c6
+license: LicenseRef-Public-Domain
+size: 118849
+timestamp: 1784250406640
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ukkonen-1.1.0-py314hd7d8586_0.conda
+sha256: 0a7efe469d7e2a34a1d017bc51cf6fb9a51436730256983694c5ad74a33bd4e0
+md5: f3a967efabf9cf450b7741487318ea6e
+depends:
+- cffi
+- libgcc >=14
+- libstdcxx >=14
+- python >=3.14,<3.15.0a0
+- python >=3.14,<3.15.0a0 *_cp314
+- python_abi 3.14.* *_cp314
+license: MIT
+license_family: MIT
+size: 15756
+timestamp: 1769438772414
+- conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-21.7.1-pyhcf101f3_0.conda
+sha256: 95a8f25bfa5505687d25913f20b1888e9512d9cd1ecc7776c1f4497654abeac2
+md5: a7e130692c42435160dd8a9071ea40d9
+depends:
+- python >=3.10
+- distlib >=0.3.7,<1
+- filelock <4,>=3.24.2
+- importlib-metadata >=6.6
+- platformdirs >=3.9.1,<5
+- python-discovery >=1.4.2
+- typing_extensions >=4.13.2
+- python
+license: MIT
+size: 3742229
+timestamp: 1785500010854
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/which-2.25-hdc560ac_0.conda
+sha256: 720691eb59b86f11ceb21b236b9402d59c47d156183375d2b24c53a201dd874b
+md5: 6dc4b55fc391a3d51ff12a6fed979562
+depends:
+- libstdcxx >=14
+- libgcc >=14
+license: GPL-3.0-only
+license_family: GPL
+size: 40249
+timestamp: 1779439555623
+- conda: https://conda.anaconda.org/conda-forge/noarch/xopen-2.1.0-pyh707e725_0.conda
+sha256: a1dc20c1315da3d4ad4e449408ec4f4aa6b73247303bd6b42c2af65512dbb60d
+md5: 8cc47651239ed7c3c9c70781c42da453
+depends:
+- __unix
+- backports.zstd
+- pbzip2
+- pigz
+- python >=3.10
+- python-isal >=1.6.1
+- python-zlib-ng >=0.4.1
+- zstd
+license: MIT
+license_family: MIT
+size: 23356
+timestamp: 1780666146275
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda
+sha256: 66265e943f32ce02396ad214e27cb35f5b0490b3bd4f064446390f9d67fa5d88
+md5: 032d8030e4a24fe1f72c74423a46fb88
+depends:
+- libgcc >=14
+license: MIT
+license_family: MIT
+size: 88088
+timestamp: 1753484092643
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda
+sha256: 210bd31c22bb88f5e2a167df24c95bb5f152b2ada7502f9b8c49d1f5366db423
+md5: ba3dcdc8584155c97c648ae9c044b7a3
+depends:
+- python >=3.10
+- python
+license: MIT
+license_family: MIT
+size: 24190
+timestamp: 1779159948016
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda
+sha256: 638a3a41a4fbfed52d3c60c8ef5a3693b3f12a5b1a3f58fa29f5698d0a0702e2
+md5: f731af71c723065d91b4c01bb822641b
+depends:
+- libgcc >=14
+- libstdcxx >=14
+license: Zlib
+license_family: Other
+size: 121046
+timestamp: 1770167944449
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda
+sha256: 569990cf12e46f9df540275146da567d9c618c1e9c7a0bc9d9cfefadaed20b75
+md5: c3655f82dcea2aa179b291e7099c1fcc
+depends:
+- libzlib >=1.3.1,<2.0a0
+license: BSD-3-Clause
+license_family: BSD
+size: 614429
+timestamp: 1764777145593
diff --git a/modules/nf-core/amulety/antiberta2/main.nf b/modules/nf-core/amulety/antiberta2/main.nf
index 571a0f89f44d..e7c6c2a73da5 100644
--- a/modules/nf-core/amulety/antiberta2/main.nf
+++ b/modules/nf-core/amulety/antiberta2/main.nf
@@ -4,9 +4,9 @@ process AMULETY_ANTIBERTA2 {
     label 'process_gpu'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/amulety_igblast:b2a7736f645c40e5':
-        'community.wave.seqera.io/library/amulety_igblast:659eaa872785adeb' }"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+?         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ae/ae2be6d5fd5a4e1024b78eb1acdfdcb6aab4326f002e98d7c2c97ef00aa979e2/data'
+:         'community.wave.seqera.io/library/amulety:1.1--5abbe5fc5e136fd3' }"
 
     input:
     tuple val(meta), path(tsv)
@@ -14,7 +14,7 @@ process AMULETY_ANTIBERTA2 {
 
     output:
     tuple val(meta), path("*.tsv"), emit: embedding
-    path "versions.yml"           , emit: versions
+    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:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/amulety/antiberta2/meta.yml b/modules/nf-core/amulety/antiberta2/meta.yml
index 9a2b7ebc7418..e3079ad33ad1 100644
--- a/modules/nf-core/amulety/antiberta2/meta.yml
+++ b/modules/nf-core/amulety/antiberta2/meta.yml
@@ -1,7 +1,5 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "amulety_antiberta2"
-description: A module to create antiberta2 embeddings of antibody (BCR) amino acid
-  sequences using amulety.
+description: A module to create antiberta2 embeddings of antibody (BCR) amino acid sequences using amulety.
 deprecated: true
 keywords:
   - embeddings
@@ -51,15 +49,52 @@ output:
 
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
+  versions_amulety:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - amulety:
+          type: string
+          description: The tool name
+      - 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:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - amulety:
+          type: string
+          description: The tool name
+      - 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"
 maintainers:
   - "@ggabernet"
+containers:
+  docker:
+    linux/arm64:
+      name: community.wave.seqera.io/library/amulety:1.1--0e94f7a12e9db539
+      build_id: bd-0e94f7a12e9db539_1
+      scan_id: sc-c46ca325fe6783e0_1
+    linux/amd64:
+      name: community.wave.seqera.io/library/amulety:1.1--5abbe5fc5e136fd3
+      build_id: bd-5abbe5fc5e136fd3_1
+      scan_id: sc-0a568678900ef142_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/amulety:1.1--e1b6039b9704c9e1
+      build_id: bd-e1b6039b9704c9e1_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ae/ae2be6d5fd5a4e1024b78eb1acdfdcb6aab4326f002e98d7c2c97ef00aa979e2/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/amulety:1.1--d896faa5bf18336b
+      build_id: bd-d896faa5bf18336b_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f0688cb48089eebe2648c1b2359e4a75a93b1e70f4580faac2173d16c61b8053/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/amulety/antiberta2/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/amulety/antiberta2/.conda-lock/linux_arm64-bd-0e94f7a12e9db539_1.txt
diff --git a/modules/nf-core/amulety/antiberty/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt b/modules/nf-core/amulety/antiberty/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
new file mode 100644
index 000000000000..a667b571ba52
--- /dev/null
+++ b/modules/nf-core/amulety/antiberty/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
@@ -0,0 +1,1830 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_3.conda
+- conda: https://conda.anaconda.org/bioconda/noarch/amulety-1.1-pyhdfd78af_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/annotated-doc-0.0.5-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/antiberty-0.1.3-pyhd8ed1ab_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.14.2-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.6.0-py314h680f03e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.7.22-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.7.22-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.1.0-py314h4a8dc5f_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/cfgv-3.5.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.4.2-pyhc90fa1f_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.6-py314hd8ed1ab_101.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.3-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.32.2-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/fmt-12.1.0-hff5e90c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/fsspec-2026.7.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-hac33072_2.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/gmpy2-2.3.0-py314h28848ee_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/h11-0.16.0-pyhcf101f3_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.4.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/hf-xet-1.5.2-py310hb823017_2.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/hpack-4.2.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/httpcore-1.0.9-pyh29332c3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/httpx-0.28.1-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/huggingface_hub-1.26.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h54a6638_2.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/identify-2.6.19-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.18-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-9.0.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.3.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/isa-l-2.32.1-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.46.1-default_hbd61a6d_102.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libabseil-20260526.0-cxx17_h7b12aa8_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-8_h5875eb1_mkl.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-8_hfef963f_mkl.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.1-hecca717_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-16.1.0-ha9f2e26_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-16.1.0-h69a702a_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.13.0-default_he001693_1000.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h3b78370_2.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-8_h5e43f62_mkl.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libprotobuf-7.35.1-h2840a7c_2.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.4-hf4e2dac_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-16.1.0-h934c35e_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-16.1.0-hdf11a46_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libtorch-2.13.0-cpu_mkl_h8bda6c0_100.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42.2-h5347b49_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libuv-1.52.1-h280c20c_0.conda
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index 000000000000..03030ea5a7cf
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+license: BSD-3-Clause
+license_family: BSD
+size: 614429
+timestamp: 1764777145593
diff --git a/modules/nf-core/amulety/antiberty/main.nf b/modules/nf-core/amulety/antiberty/main.nf
index 274cdbff5c08..255ed21522ef 100644
--- a/modules/nf-core/amulety/antiberty/main.nf
+++ b/modules/nf-core/amulety/antiberty/main.nf
@@ -4,9 +4,9 @@ process AMULETY_ANTIBERTY {
     label 'process_gpu'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/amulety_igblast:b2a7736f645c40e5':
-        'community.wave.seqera.io/library/amulety_igblast:659eaa872785adeb' }"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+?         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ae/ae2be6d5fd5a4e1024b78eb1acdfdcb6aab4326f002e98d7c2c97ef00aa979e2/data'
+:         'community.wave.seqera.io/library/amulety:1.1--5abbe5fc5e136fd3' }"
 
     input:
     tuple val(meta), path(tsv)
@@ -14,7 +14,7 @@ process AMULETY_ANTIBERTY {
 
     output:
     tuple val(meta), path("*.tsv"), emit: embedding
-    path "versions.yml"           , emit: versions
+    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:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/amulety/antiberty/meta.yml b/modules/nf-core/amulety/antiberty/meta.yml
index 344d8bbf54f3..7e22d2ce0ab9 100644
--- a/modules/nf-core/amulety/antiberty/meta.yml
+++ b/modules/nf-core/amulety/antiberty/meta.yml
@@ -1,7 +1,5 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "amulety_antiberty"
-description: A module to create antiberty embeddings of antibody (BCR) amino acid
-  sequences using amulety.
+description: A module to create antiberty embeddings of antibody (BCR) amino acid sequences using amulety.
 deprecated: true
 keywords:
   - embeddings
@@ -51,15 +49,52 @@ output:
 
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
+  versions_amulety:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - amulety:
+          type: string
+          description: The tool name
+      - 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:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - amulety:
+          type: string
+          description: The tool name
+      - 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"
 maintainers:
   - "@ggabernet"
+containers:
+  docker:
+    linux/amd64:
+      name: community.wave.seqera.io/library/amulety:1.1--5abbe5fc5e136fd3
+      build_id: bd-5abbe5fc5e136fd3_1
+      scan_id: sc-0a568678900ef142_1
+    linux/arm64:
+      name: community.wave.seqera.io/library/amulety:1.1--0e94f7a12e9db539
+      build_id: bd-0e94f7a12e9db539_1
+      scan_id: sc-c46ca325fe6783e0_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/amulety:1.1--e1b6039b9704c9e1
+      build_id: bd-e1b6039b9704c9e1_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ae/ae2be6d5fd5a4e1024b78eb1acdfdcb6aab4326f002e98d7c2c97ef00aa979e2/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/amulety:1.1--d896faa5bf18336b
+      build_id: bd-d896faa5bf18336b_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f0688cb48089eebe2648c1b2359e4a75a93b1e70f4580faac2173d16c61b8053/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/amulety/antiberty/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/amulety/antiberty/.conda-lock/linux_arm64-bd-0e94f7a12e9db539_1.txt
diff --git a/modules/nf-core/amulety/balmpaired/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt b/modules/nf-core/amulety/balmpaired/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
new file mode 100644
index 000000000000..a667b571ba52
--- /dev/null
+++ b/modules/nf-core/amulety/balmpaired/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
@@ -0,0 +1,1830 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_3.conda
+- conda: https://conda.anaconda.org/bioconda/noarch/amulety-1.1-pyhdfd78af_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/annotated-doc-0.0.5-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/antiberty-0.1.3-pyhd8ed1ab_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.14.2-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.6.0-py314h680f03e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.7.22-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.7.22-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.1.0-py314h4a8dc5f_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/cfgv-3.5.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.4.2-pyhc90fa1f_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.6-py314hd8ed1ab_101.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.3-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.32.2-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/fmt-12.1.0-hff5e90c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/fsspec-2026.7.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-hac33072_2.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/gmpy2-2.3.0-py314h28848ee_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/h11-0.16.0-pyhcf101f3_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.4.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/hf-xet-1.5.2-py310hb823017_2.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/hpack-4.2.0-pyhd8ed1ab_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libprotobuf-7.35.1-h2840a7c_2.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/libuv-1.52.1-h280c20c_0.conda
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index 000000000000..03030ea5a7cf
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+sha256: 9cf704a4e09dec66427b30652469897406cabb1e8b8bc607818f2ccd20365ede
+md5: 820bbc61438897725bc4328638c07dbe
+depends:
+- libgcc >=14
+- python >=3.14,<3.15.0a0
+- python_abi 3.14.* *_cp314
+constrains:
+- __glibc >=2.17
+license: MIT
+license_family: MIT
+size: 3225604
+timestamp: 1762187827210
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/rpds-py-2026.6.3-py314h721bf50_0.conda
+sha256: 1ff570c281f01fb44ce1f98be767861eb576b5124ae10c6a6e8ba49170ddffac
+md5: 2c1fc56e44a3c0e7b7d22f3beafd18ca
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+- python
+- libgcc >=14
+- python_abi 3.14.* *_cp314
+constrains:
+- __glibc >=2.17
+license: MIT
+license_family: MIT
+size: 295329
+timestamp: 1782831266058
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/safetensors-0.8.0-py314h02b7a91_0.conda
+sha256: 80f088dc7502feb2e239cc265950bcdeaf94106f562726655fb3fe7f396136fa
+md5: baca7264fdb2ef68ab5d9b9093505e1d
+depends:
+- python
+- libgcc >=14
+- python_abi 3.14.* *_cp314
+constrains:
+- __glibc >=2.17
+license: Apache-2.0
+license_family: APACHE
+size: 490922
+timestamp: 1781179708027
+- conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-81.0.0-pyh332efcf_0.conda
+sha256: 6ecf738d5590bf228f09c4ecd1ea91d811f8e0bd9acdef341bc4d6c36beb13a3
+md5: d629a398d7bf872f9ed7b27ab959de15
+depends:
+- python >=3.10
+license: MIT
+license_family: MIT
+size: 676888
+timestamp: 1770456470072
+- conda: https://conda.anaconda.org/conda-forge/noarch/shellingham-1.5.4-pyhd8ed1ab_2.conda
+sha256: 1d6534df8e7924d9087bd388fbac5bd868c5bf8971c36885f9f016da0657d22b
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+depends:
+- python >=3.10
+license: MIT
+license_family: MIT
+size: 15018
+timestamp: 1762858315311
+- conda: https://conda.anaconda.org/conda-forge/noarch/six-1.17.0-pyhe01879c_1.conda
+sha256: 458227f759d5e3fcec5d9b7acce54e10c9e1f4f4b7ec978f3bfd54ce4ee9853d
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+depends:
+- python >=3.9
+- python
+license: MIT
+license_family: MIT
+size: 18455
+timestamp: 1753199211006
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sleef-3.9.0-h5bb93e2_0.conda
+sha256: 8292f6d40541d136fe3c525062db5f2ec584e442e4c8b60296b630bbe85cadce
+md5: b90e82764e7de5a291e263ead7950ad4
+depends:
+- _openmp_mutex >=4.5
+- libgcc >=14
+- libstdcxx >=14
+license: BSL-1.0
+size: 1190849
+timestamp: 1756276271706
+- conda: https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.1-pyhd8ed1ab_2.conda
+sha256: dce518f45e24cd03f401cb0616917773159a210c19d601c5f2d4e0e5879d30ad
+md5: 03fe290994c5e4ec17293cfb6bdce520
+depends:
+- python >=3.10
+license: Apache-2.0
+license_family: Apache
+size: 15698
+timestamp: 1762941572482
+- conda: https://conda.anaconda.org/conda-forge/noarch/sympy-1.14.0-pyh2585a3b_106.conda
+sha256: 1c8057e6875eba958aa8b3c1a072dc9a75d013f209c26fd8125a5ebd3abbec0c
+md5: 32d866e43b25275f61566b9391ccb7b5
+depends:
+- __unix
+- cpython
+- gmpy2 >=2.0.8
+- mpmath >=1.1.0,<1.5
+- python >=3.10
+license: BSD-3-Clause
+license_family: BSD
+size: 4661767
+timestamp: 1771952371059
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.13-noxft_h5cf4473_3.conda
+build_number: 103
+sha256: cd51fbda051a9f3679d10ef4a94cd1ff38c10533b82845dadce8ba87245ba4ce
+md5: 89e78452e06563964e419059ee45584a
+depends:
+- libgcc >=14
+- libzlib >=1.3.2,<2.0a0
+constrains:
+- xorg-libx11 >=1.8.13,<2.0a0
+license: TCL
+size: 3683040
+timestamp: 1784229053797
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/tokenizers-0.22.2-py314h56f8308_0.conda
+sha256: 59fe996e2d860ec2a30bb5f204c5c807735eb2fb7aa4ab491f79053de28a5b15
+md5: 8784f3a566787f27a705f304e8357aa1
+depends:
+- huggingface_hub >=0.16.4,<2.0
+- libgcc >=14
+- libstdcxx >=14
+- openssl >=3.5.4,<4.0a0
+- python >=3.14,<3.15.0a0
+- python >=3.14,<3.15.0a0 *_cp314
+- python_abi 3.14.* *_cp314
+constrains:
+- __glibc >=2.17
+license: Apache-2.0
+license_family: APACHE
+size: 2438359
+timestamp: 1764695098756
+- conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.4.1-pyhcf101f3_0.conda
+sha256: 91cafdb64268e43e0e10d30bd1bef5af392e69f00edd34dfaf909f69ab2da6bd
+md5: b5325cf06a000c5b14970462ff5e4d58
+depends:
+- python >=3.10
+- python
+license: MIT
+license_family: MIT
+size: 21561
+timestamp: 1774492402955
+- conda: https://conda.anaconda.org/conda-forge/noarch/tqdm-4.70.0-pyh8f84b5b_0.conda
+sha256: a4d9e9da15b13f1ab047e7db412e2ed564bc615832e80213cf129b973c3abf4a
+md5: 00953c3b729e03b0ae21f49fdf3441bb
+depends:
+- python >=3.10
+- __unix
+- python
+constrains:
+- envwrap >=0.2
+- ipywidgets >=6.0
+license: MPL-2.0 and MIT
+size: 98184
+timestamp: 1785172528905
+- conda: https://conda.anaconda.org/conda-forge/noarch/transformers-5.14.1-pyhcf101f3_0.conda
+sha256: aca27f98965064da34c0baa63c5d69cbe84fb85607b3c45af37f7e3ee6bf4c7e
+md5: e9a596eee896e0b5525054aaff759c3a
+depends:
+- python >=3.10
+- huggingface_hub >=1.5.0,<2.0
+- numpy >=1.17
+- packaging >=20.0
+- pyyaml >=5.1
+- regex >=2025.10.22
+- tokenizers >=0.22.0,<=0.23.0
+- typer
+- safetensors >=0.8.0
+- tqdm >=4.60
+- python
+license: Apache-2.0
+license_family: APACHE
+size: 4397095
+timestamp: 1784221007396
+- conda: https://conda.anaconda.org/conda-forge/noarch/typer-0.27.0-pyhcf101f3_0.conda
+sha256: f44984374b248c45f7e3d43a2cb0bf73d1441ecea07fb73198e89f643f6c5824
+md5: aa0ef00569728be93656de5f097fc81d
+depends:
+- annotated-doc >=0.0.2
+- colorama
+- python >=3.10
+- rich >=13.8.0
+- shellingham >=1.3.0
+- python
+license: MIT AND BSD-3-Clause
+size: 187450
+timestamp: 1784167351535
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.16.0-h69aa097_0.conda
+sha256: b141933ece3518f6d7b75dfb59451e2f26b405a44c18e2518a83e9a02e09315c
+md5: c680b5747e8c4c8f23dca0bb7042a8fc
+depends:
+- typing_extensions ==4.16.0 pyhcf101f3_0
+license: PSF-2.0
+license_family: PSF
+size: 94080
+timestamp: 1783002732887
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.16.0-pyhcf101f3_0.conda
+sha256: 2d888f90af0686044882c74193ec80a90ec1943145d94a7b1b048958acda1848
+md5: c70ad746c22219b9700931707482992c
+depends:
+- python >=3.10
+- python
+license: PSF-2.0
+license_family: PSF
+size: 52631
+timestamp: 1783002732887
+- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2026c-h151e31d_0.conda
+sha256: b928c30ddcb0e3f544c6eade8352737e6e610e263276b90232db6a578ef899d8
+md5: fcb489df604d100968b737f2cb6076c6
+license: LicenseRef-Public-Domain
+size: 118849
+timestamp: 1784250406640
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ukkonen-1.1.0-py314hd7d8586_0.conda
+sha256: 0a7efe469d7e2a34a1d017bc51cf6fb9a51436730256983694c5ad74a33bd4e0
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+depends:
+- cffi
+- libgcc >=14
+- libstdcxx >=14
+- python >=3.14,<3.15.0a0
+- python >=3.14,<3.15.0a0 *_cp314
+- python_abi 3.14.* *_cp314
+license: MIT
+license_family: MIT
+size: 15756
+timestamp: 1769438772414
+- conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-21.7.1-pyhcf101f3_0.conda
+sha256: 95a8f25bfa5505687d25913f20b1888e9512d9cd1ecc7776c1f4497654abeac2
+md5: a7e130692c42435160dd8a9071ea40d9
+depends:
+- python >=3.10
+- distlib >=0.3.7,<1
+- filelock <4,>=3.24.2
+- importlib-metadata >=6.6
+- platformdirs >=3.9.1,<5
+- python-discovery >=1.4.2
+- typing_extensions >=4.13.2
+- python
+license: MIT
+size: 3742229
+timestamp: 1785500010854
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/which-2.25-hdc560ac_0.conda
+sha256: 720691eb59b86f11ceb21b236b9402d59c47d156183375d2b24c53a201dd874b
+md5: 6dc4b55fc391a3d51ff12a6fed979562
+depends:
+- libstdcxx >=14
+- libgcc >=14
+license: GPL-3.0-only
+license_family: GPL
+size: 40249
+timestamp: 1779439555623
+- conda: https://conda.anaconda.org/conda-forge/noarch/xopen-2.1.0-pyh707e725_0.conda
+sha256: a1dc20c1315da3d4ad4e449408ec4f4aa6b73247303bd6b42c2af65512dbb60d
+md5: 8cc47651239ed7c3c9c70781c42da453
+depends:
+- __unix
+- backports.zstd
+- pbzip2
+- pigz
+- python >=3.10
+- python-isal >=1.6.1
+- python-zlib-ng >=0.4.1
+- zstd
+license: MIT
+license_family: MIT
+size: 23356
+timestamp: 1780666146275
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda
+sha256: 66265e943f32ce02396ad214e27cb35f5b0490b3bd4f064446390f9d67fa5d88
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+- libgcc >=14
+license: MIT
+license_family: MIT
+size: 88088
+timestamp: 1753484092643
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda
+sha256: 210bd31c22bb88f5e2a167df24c95bb5f152b2ada7502f9b8c49d1f5366db423
+md5: ba3dcdc8584155c97c648ae9c044b7a3
+depends:
+- python >=3.10
+- python
+license: MIT
+license_family: MIT
+size: 24190
+timestamp: 1779159948016
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda
+sha256: 638a3a41a4fbfed52d3c60c8ef5a3693b3f12a5b1a3f58fa29f5698d0a0702e2
+md5: f731af71c723065d91b4c01bb822641b
+depends:
+- libgcc >=14
+- libstdcxx >=14
+license: Zlib
+license_family: Other
+size: 121046
+timestamp: 1770167944449
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda
+sha256: 569990cf12e46f9df540275146da567d9c618c1e9c7a0bc9d9cfefadaed20b75
+md5: c3655f82dcea2aa179b291e7099c1fcc
+depends:
+- libzlib >=1.3.1,<2.0a0
+license: BSD-3-Clause
+license_family: BSD
+size: 614429
+timestamp: 1764777145593
diff --git a/modules/nf-core/amulety/balmpaired/main.nf b/modules/nf-core/amulety/balmpaired/main.nf
index 6b5788af76bd..7efb34a69399 100644
--- a/modules/nf-core/amulety/balmpaired/main.nf
+++ b/modules/nf-core/amulety/balmpaired/main.nf
@@ -4,9 +4,9 @@ process AMULETY_BALMPAIRED {
     label 'process_gpu'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/amulety_wget:d69a2bc09a42a8b2':
-        'community.wave.seqera.io/library/amulety_wget:2ecd2554d8d6f58e' }"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+?         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ae/ae2be6d5fd5a4e1024b78eb1acdfdcb6aab4326f002e98d7c2c97ef00aa979e2/data'
+:         'community.wave.seqera.io/library/amulety:1.1--5abbe5fc5e136fd3' }"
 
     input:
     tuple val(meta), path(tsv)
@@ -14,7 +14,7 @@ process AMULETY_BALMPAIRED {
 
     output:
     tuple val(meta), path("*.tsv"), emit: embedding
-    path "versions.yml"           , emit: versions
+    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:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/amulety/balmpaired/meta.yml b/modules/nf-core/amulety/balmpaired/meta.yml
index 2464b12ef39d..a297564f7035 100644
--- a/modules/nf-core/amulety/balmpaired/meta.yml
+++ b/modules/nf-core/amulety/balmpaired/meta.yml
@@ -1,7 +1,5 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "amulety_balmpaired"
-description: A module to create BALM paired embeddings of antibody (BCR) amino acid
-  sequences using amulety.
+description: A module to create BALM paired embeddings of antibody (BCR) amino acid sequences using amulety.
 deprecated: true
 keywords:
   - embeddings
@@ -51,15 +49,52 @@ output:
 
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
+  versions_amulety:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - amulety:
+          type: string
+          description: The tool name
+      - 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:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - amulety:
+          type: string
+          description: The tool name
+      - 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"
 maintainers:
   - "@ggabernet"
+containers:
+  docker:
+    linux/arm64:
+      name: community.wave.seqera.io/library/amulety:1.1--0e94f7a12e9db539
+      build_id: bd-0e94f7a12e9db539_1
+      scan_id: sc-c46ca325fe6783e0_1
+    linux/amd64:
+      name: community.wave.seqera.io/library/amulety:1.1--5abbe5fc5e136fd3
+      build_id: bd-5abbe5fc5e136fd3_1
+      scan_id: sc-0a568678900ef142_1
+  singularity:
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/amulety:1.1--d896faa5bf18336b
+      build_id: bd-d896faa5bf18336b_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f0688cb48089eebe2648c1b2359e4a75a93b1e70f4580faac2173d16c61b8053/data
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/amulety:1.1--e1b6039b9704c9e1
+      build_id: bd-e1b6039b9704c9e1_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ae/ae2be6d5fd5a4e1024b78eb1acdfdcb6aab4326f002e98d7c2c97ef00aa979e2/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/amulety/balmpaired/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/amulety/balmpaired/.conda-lock/linux_arm64-bd-0e94f7a12e9db539_1.txt
diff --git a/modules/nf-core/amulety/esm2/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt b/modules/nf-core/amulety/esm2/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
new file mode 100644
index 000000000000..a667b571ba52
--- /dev/null
+++ b/modules/nf-core/amulety/esm2/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
@@ -0,0 +1,1830 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-7_kmp_llvm.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_3.conda
+- conda: https://conda.anaconda.org/bioconda/noarch/amulety-1.1-pyhdfd78af_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/annotated-doc-0.0.5-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/antiberty-0.1.3-pyhd8ed1ab_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.14.2-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.6.0-py314h680f03e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.7.22-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.7.22-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.1.0-py314h4a8dc5f_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/cfgv-3.5.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.4.2-pyhc90fa1f_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.6-py314hd8ed1ab_101.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.3-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.32.2-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/fmt-12.1.0-hff5e90c_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.16.0-pyhcf101f3_0.conda
+sha256: 2d888f90af0686044882c74193ec80a90ec1943145d94a7b1b048958acda1848
+md5: c70ad746c22219b9700931707482992c
+depends:
+- python >=3.10
+- python
+license: PSF-2.0
+license_family: PSF
+size: 52631
+timestamp: 1783002732887
+- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2026c-h151e31d_0.conda
+sha256: b928c30ddcb0e3f544c6eade8352737e6e610e263276b90232db6a578ef899d8
+md5: fcb489df604d100968b737f2cb6076c6
+license: LicenseRef-Public-Domain
+size: 118849
+timestamp: 1784250406640
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/ukkonen-1.1.0-py314hd7d8586_0.conda
+sha256: 0a7efe469d7e2a34a1d017bc51cf6fb9a51436730256983694c5ad74a33bd4e0
+md5: f3a967efabf9cf450b7741487318ea6e
+depends:
+- cffi
+- libgcc >=14
+- libstdcxx >=14
+- python >=3.14,<3.15.0a0
+- python >=3.14,<3.15.0a0 *_cp314
+- python_abi 3.14.* *_cp314
+license: MIT
+license_family: MIT
+size: 15756
+timestamp: 1769438772414
+- conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-21.7.1-pyhcf101f3_0.conda
+sha256: 95a8f25bfa5505687d25913f20b1888e9512d9cd1ecc7776c1f4497654abeac2
+md5: a7e130692c42435160dd8a9071ea40d9
+depends:
+- python >=3.10
+- distlib >=0.3.7,<1
+- filelock <4,>=3.24.2
+- importlib-metadata >=6.6
+- platformdirs >=3.9.1,<5
+- python-discovery >=1.4.2
+- typing_extensions >=4.13.2
+- python
+license: MIT
+size: 3742229
+timestamp: 1785500010854
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/which-2.25-hdc560ac_0.conda
+sha256: 720691eb59b86f11ceb21b236b9402d59c47d156183375d2b24c53a201dd874b
+md5: 6dc4b55fc391a3d51ff12a6fed979562
+depends:
+- libstdcxx >=14
+- libgcc >=14
+license: GPL-3.0-only
+license_family: GPL
+size: 40249
+timestamp: 1779439555623
+- conda: https://conda.anaconda.org/conda-forge/noarch/xopen-2.1.0-pyh707e725_0.conda
+sha256: a1dc20c1315da3d4ad4e449408ec4f4aa6b73247303bd6b42c2af65512dbb60d
+md5: 8cc47651239ed7c3c9c70781c42da453
+depends:
+- __unix
+- backports.zstd
+- pbzip2
+- pigz
+- python >=3.10
+- python-isal >=1.6.1
+- python-zlib-ng >=0.4.1
+- zstd
+license: MIT
+license_family: MIT
+size: 23356
+timestamp: 1780666146275
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda
+sha256: 66265e943f32ce02396ad214e27cb35f5b0490b3bd4f064446390f9d67fa5d88
+md5: 032d8030e4a24fe1f72c74423a46fb88
+depends:
+- libgcc >=14
+license: MIT
+license_family: MIT
+size: 88088
+timestamp: 1753484092643
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda
+sha256: 210bd31c22bb88f5e2a167df24c95bb5f152b2ada7502f9b8c49d1f5366db423
+md5: ba3dcdc8584155c97c648ae9c044b7a3
+depends:
+- python >=3.10
+- python
+license: MIT
+license_family: MIT
+size: 24190
+timestamp: 1779159948016
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda
+sha256: 638a3a41a4fbfed52d3c60c8ef5a3693b3f12a5b1a3f58fa29f5698d0a0702e2
+md5: f731af71c723065d91b4c01bb822641b
+depends:
+- libgcc >=14
+- libstdcxx >=14
+license: Zlib
+license_family: Other
+size: 121046
+timestamp: 1770167944449
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda
+sha256: 569990cf12e46f9df540275146da567d9c618c1e9c7a0bc9d9cfefadaed20b75
+md5: c3655f82dcea2aa179b291e7099c1fcc
+depends:
+- libzlib >=1.3.1,<2.0a0
+license: BSD-3-Clause
+license_family: BSD
+size: 614429
+timestamp: 1764777145593
diff --git a/modules/nf-core/amulety/esm2/main.nf b/modules/nf-core/amulety/esm2/main.nf
index 85b30fa221ef..63d7b516af10 100644
--- a/modules/nf-core/amulety/esm2/main.nf
+++ b/modules/nf-core/amulety/esm2/main.nf
@@ -4,9 +4,9 @@ process AMULETY_ESM2 {
     label 'process_gpu'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/amulety_igblast:b2a7736f645c40e5':
-        'community.wave.seqera.io/library/amulety_igblast:659eaa872785adeb' }"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+?         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ae/ae2be6d5fd5a4e1024b78eb1acdfdcb6aab4326f002e98d7c2c97ef00aa979e2/data'
+:         'community.wave.seqera.io/library/amulety:1.1--5abbe5fc5e136fd3' }"
 
     input:
     tuple val(meta), path(tsv)
@@ -14,7 +14,7 @@ process AMULETY_ESM2 {
 
     output:
     tuple val(meta), path("*.tsv"), emit: embedding
-    path "versions.yml"           , emit: versions
+    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:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/amulety/esm2/meta.yml b/modules/nf-core/amulety/esm2/meta.yml
index 9233777ffa22..03174ce90811 100644
--- a/modules/nf-core/amulety/esm2/meta.yml
+++ b/modules/nf-core/amulety/esm2/meta.yml
@@ -1,7 +1,5 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "amulety_esm2"
-description: A module to create esm2 embeddings of antibody (BCR) amino acid sequences
-  using amulety.
+description: A module to create esm2 embeddings of antibody (BCR) amino acid sequences using amulety.
 deprecated: true
 keywords:
   - embeddings
@@ -51,15 +49,52 @@ output:
 
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
+  versions_amulety:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - amulety:
+          type: string
+          description: The tool name
+      - 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:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - amulety:
+          type: string
+          description: The tool name
+      - 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"
 maintainers:
   - "@ggabernet"
+containers:
+  docker:
+    linux/arm64:
+      name: community.wave.seqera.io/library/amulety:1.1--0e94f7a12e9db539
+      build_id: bd-0e94f7a12e9db539_1
+      scan_id: sc-c46ca325fe6783e0_1
+    linux/amd64:
+      name: community.wave.seqera.io/library/amulety:1.1--5abbe5fc5e136fd3
+      build_id: bd-5abbe5fc5e136fd3_1
+      scan_id: sc-0a568678900ef142_1
+  singularity:
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/amulety:1.1--d896faa5bf18336b
+      build_id: bd-d896faa5bf18336b_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f0688cb48089eebe2648c1b2359e4a75a93b1e70f4580faac2173d16c61b8053/data
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/amulety:1.1--e1b6039b9704c9e1
+      build_id: bd-e1b6039b9704c9e1_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ae/ae2be6d5fd5a4e1024b78eb1acdfdcb6aab4326f002e98d7c2c97ef00aa979e2/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/amulety/esm2/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/amulety/esm2/.conda-lock/linux_arm64-bd-0e94f7a12e9db539_1.txt