Skip to content

Amulety modules bump versions #11645

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ggabernet wants to merge 24 commits into
base: master
Choose a base branch
from
Open

Amulety modules bump versions #11645

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
24 commits
Select commit Hold shift + click to select a range
df9b2e2
update amulety version
ggabernet Jan 26, 2026
45ff2e1
update snapshot
ggabernet Jan 26, 2026
29b1939
update singularity oras to https
ggabernet Jan 29, 2026
a872cc2
Merge branch 'master' of https://github.com/nf-core/modules into amulety
ggabernet Jan 29, 2026
3479af5
update container
ggabernet Jan 29, 2026
8eceb3c
fix amulety GPU support
ggabernet Mar 10, 2026
84b9e53
Merge branch 'master' into amulety
ggabernet Mar 10, 2026
a7b7872
fix container GPU
ggabernet Mar 11, 2026
79ab72d
Merge branch 'amulety' of https://github.com/ggabernet/nf-core-module…
ggabernet Mar 11, 2026
3af04ec
merge upstream
ggabernet Mar 11, 2026
c3b3bb1
Merge branch 'master' into amulety
ggabernet Mar 11, 2026
a4a04fe
fix meta
ggabernet Mar 11, 2026
1a91ef6
fix linting
ggabernet Mar 11, 2026
da6e643
Merge branch 'amulety' of https://github.com/ggabernet/nf-core-module…
ggabernet Mar 11, 2026
7e3436b
update snapshots
ggabernet Mar 12, 2026
9e9feac
Merge branch 'master' into amulety
ggabernet Mar 12, 2026
40dc808
update stub snapshot
ggabernet Mar 12, 2026
a52e72a
Merge branch 'amulety' of https://github.com/ggabernet/nf-core-module…
ggabernet Mar 12, 2026
84c6d20
Merge branch 'master' of https://github.com/nf-core/modules into amulety
ggabernet May 14, 2026
2a43fb6
update amulety version
ggabernet May 14, 2026
193c0ad
update snapshot
ggabernet May 14, 2026
79f78ad
Merge branch 'master' into amulety
ggabernet May 14, 2026
dd900a0
update gpu snapshot
ggabernet May 14, 2026
6723743
Merge branch 'amulety' of https://github.com/ggabernet/nf-core-module…
ggabernet May 14, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions modules/nf-core/amulety/embed/environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Copy link
Copy Markdown
Contributor

@mashehu mashehu May 14, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

You should also pin the version of pip from conda-forge

- amulety==2.1.2
- torch==2.10.0
- amulety==2.1.3
Copy link
Copy Markdown
Contributor

@mashehu mashehu May 14, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

These other tool versions should also be emitted

- torch==2.12.0
- transformers==4.49.0
4 changes: 2 additions & 2 deletions modules/nf-core/amulety/embed/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
24 changes: 12 additions & 12 deletions modules/nf-core/amulety/embed/tests/gpu.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
"id": "test",
"single_end": false
},
"test.tsv:md5,8ed0c1c7e8acc1bd8a5b3099c3cc0e53"
"test.tsv:md5,1feb3fbc43aae1bb51d45e3552372240"
]
],
"1": [
Expand All @@ -24,7 +24,7 @@
[
"AMULETY_EMBED",
"amulety",
"2.1.2"
"2.1.3"
]
],
"embedding": [
Expand All @@ -33,7 +33,7 @@
"id": "test",
"single_end": false
},
"test.tsv:md5,8ed0c1c7e8acc1bd8a5b3099c3cc0e53"
"test.tsv:md5,1feb3fbc43aae1bb51d45e3552372240"
]
],
"embedding_metadata": [
Expand All @@ -49,16 +49,16 @@
[
"AMULETY_EMBED",
"amulety",
"2.1.2"
"2.1.3"
]
]
}
],
"timestamp": "2026-05-14T10:40:36.138512029",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-03-12T13:33:07.008006758"
"nf-test": "0.9.5",
"nextflow": "26.04.1"
}
},
"human - AIRR rearrangement - stub": {
"content": [
Expand All @@ -85,7 +85,7 @@
[
"AMULETY_EMBED",
"amulety",
"2.1.2"
"2.1.3"
]
],
"embedding": [
Expand All @@ -110,15 +110,15 @@
[
"AMULETY_EMBED",
"amulety",
"2.1.2"
"2.1.3"
]
]
}
],
"timestamp": "2026-03-12T13:33:18.34555436",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-03-12T13:33:18.34555436"
}
}
}
20 changes: 10 additions & 10 deletions modules/nf-core/amulety/embed/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@
[
"AMULETY_EMBED",
"amulety",
"2.1.2"
"2.1.3"
]
],
"embedding": [
Expand All @@ -49,16 +49,16 @@
[
"AMULETY_EMBED",
"amulety",
"2.1.2"
"2.1.3"
]
]
}
],
"timestamp": "2026-05-14T10:41:03.994719942",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-03-12T13:33:37.430813005"
"nf-test": "0.9.5",
"nextflow": "26.04.1"
}
},
"human - AIRR rearrangement - stub": {
"content": [
Expand All @@ -85,7 +85,7 @@
[
"AMULETY_EMBED",
"amulety",
"2.1.2"
"2.1.3"
]
],
"embedding": [
Expand All @@ -110,15 +110,15 @@
[
"AMULETY_EMBED",
"amulety",
"2.1.2"
"2.1.3"
]
]
}
],
"timestamp": "2026-03-12T13:33:48.628764499",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-03-12T13:33:48.628764499"
}
}
}
4 changes: 2 additions & 2 deletions modules/nf-core/amulety/translate/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/amulety/translate/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
[
"AMULETY_TRANSLATE",
"amulety",
"2.1.2"
"2.1.3"
]
],
"2": [
Expand All @@ -36,7 +36,7 @@
[
"AMULETY_TRANSLATE",
"amulety",
"2.1.2"
"2.1.3"
]
],
"versions_igblastn": [
Expand Down Expand Up @@ -69,7 +69,7 @@
[
"AMULETY_TRANSLATE",
"amulety",
"2.1.2"
"2.1.3"
]
],
"2": [
Expand All @@ -91,7 +91,7 @@
[
"AMULETY_TRANSLATE",
"amulety",
"2.1.2"
"2.1.3"
]
],
"versions_igblastn": [
Expand Down
Loading