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Migrate amulety to topics #12481

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72b37fc
chore: migrate amulety to topics
atrigila Jul 31, 2026
5358720
replacce oras containers for https
atrigila Jul 31, 2026
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1,830 changes: 1,830 additions & 0 deletions modules/nf-core/amulety/antiberta2/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
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1,727 changes: 1,727 additions & 0 deletions modules/nf-core/amulety/antiberta2/.conda-lock/linux_arm64-bd-0e94f7a12e9db539_1.txt
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8 changes: 4 additions & 4 deletions modules/nf-core/amulety/antiberta2/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,17 +4,17 @@ 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)
val(chain)

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
Expand Down
55 changes: 45 additions & 10 deletions modules/nf-core/amulety/antiberta2/meta.yml
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Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -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
1,830 changes: 1,830 additions & 0 deletions modules/nf-core/amulety/antiberty/.conda-lock/linux_amd64-bd-5abbe5fc5e136fd3_1.txt
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1,727 changes: 1,727 additions & 0 deletions modules/nf-core/amulety/antiberty/.conda-lock/linux_arm64-bd-0e94f7a12e9db539_1.txt
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8 changes: 4 additions & 4 deletions modules/nf-core/amulety/antiberty/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,17 +4,17 @@ 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)
val(chain)

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
Expand Down
55 changes: 45 additions & 10 deletions modules/nf-core/amulety/antiberty/meta.yml
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Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -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
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