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Update bakta modules to 1.120 #12041

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Merged
jfy133 merged 27 commits into from
Jun 22, 2026
Merged

Update bakta modules to 1.120 #12041

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1fc3a15
Update Kaiju to also emit the downstream required nodes file
jfy133 Apr 14, 2026
71a59d9
Include names file as well
jfy133 Apr 14, 2026
76f71ac
Merge branch 'master' into master
jfy133 Apr 14, 2026
3f2eda9
Update documentation
jfy133 Apr 14, 2026
3cf6c1e
Merge branch 'master' of github.com:jfy133/nf-core-modules
jfy133 Apr 14, 2026
e59b17a
Merge branch 'master' into master
jfy133 Apr 15, 2026
f4ff336
update all Kaiju modules to topics
jfy133 Apr 15, 2026
9513f48
Remove debug thing from sourmash
jfy133 Apr 15, 2026
29d66bd
Reset KMCP files
jfy133 Apr 15, 2026
a55b830
[automated] Fix code linting
nf-core-bot Apr 17, 2026
8bcaaa5
Merge branch 'nf-core:master' into master
jfy133 Apr 20, 2026
13f5aad
Merge branch 'nf-core:master' into master
jfy133 Apr 20, 2026
d3ac768
Merge branch 'nf-core:master' into master
jfy133 Apr 24, 2026
9bcbf39
Merge branch 'nf-core:master' into master
jfy133 Apr 29, 2026
4c1868d
Merge branch 'nf-core:master' into master
jfy133 May 17, 2026
297dada
Merge branch 'nf-core:master' into master
jfy133 Jun 17, 2026
7db4592
Snbapshot update bakta.bakta
jfy133 Jun 17, 2026
b6a3e87
update snapshots
jfy133 Jun 18, 2026
6cde181
Improve slightly the version capture to ignore weird error on GHA
jfy133 Jun 18, 2026
754eb4a
Try defining fontconfig path to get around container issues
jfy133 Jun 18, 2026
b5fa223
Try fix linting
jfy133 Jun 18, 2026
1f1bce4
Try another cache lcoation...
jfy133 Jun 18, 2026
2b63701
Merge branch 'master' into update-bakta
jfy133 Jun 18, 2026
f29960e
Try making the cache directories?
jfy133 Jun 18, 2026
d4d86e4
Use fake home
jfy133 Jun 22, 2026
9164b70
Merge branch 'update-bakta' of github.com:jfy133/nf-core-modules into…
jfy133 Jun 22, 2026
99eb90f
Merge branch 'master' into update-bakta
jfy133 Jun 22, 2026
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3 changes: 2 additions & 1 deletion modules/nf-core/bakta/bakta/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::bakta=1.11.4
- bioconda::bakta=1.12.0
- bioconda::diamond=2.2.0
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4 changes: 2 additions & 2 deletions modules/nf-core/bakta/bakta/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process BAKTA_BAKTA {

conda "${moduleDir}/environment.yml"
container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/bakta:1.11.4--pyhdfd78af_0'
: 'quay.io/biocontainers/bakta:1.11.4--pyhdfd78af_0'}"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/50/50b75335f6394ae83fd05f364db27ee2eb75f4170e3525bb2aea47ad717a9e64/data'
: 'community.wave.seqera.io/library/bakta_diamond:7830b94718da4f96'}"

input:
tuple val(meta), path(fasta)
Expand Down
16 changes: 8 additions & 8 deletions modules/nf-core/bakta/bakta/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -6,15 +6,15 @@
[
"BAKTA_BAKTA",
"bakta",
"1.11.4"
"1.12.0"
]
]
}
],
"timestamp": "2026-03-17T21:20:19.285606344",
"timestamp": "2026-06-17T15:40:47.396215774",
"meta": {
"nf-test": "0.9.4",
"nextflow": "26.02.0"
"nf-test": "0.9.5",
"nextflow": "26.04.3"
}
},
"Bakta - stub": {
Expand Down Expand Up @@ -104,15 +104,15 @@
[
"BAKTA_BAKTA",
"bakta",
"1.11.4"
"1.12.0"
]
]
}
],
"timestamp": "2026-03-17T21:20:30.005281737",
"timestamp": "2026-06-17T12:15:36.61419838",
"meta": {
"nf-test": "0.9.4",
"nextflow": "26.02.0"
"nf-test": "0.9.5",
"nextflow": "26.04.3"
}
}
}
3 changes: 2 additions & 1 deletion modules/nf-core/bakta/baktadbdownload/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::bakta=1.11.4
- bioconda::bakta=1.12.0
- bioconda::diamond=2.2.0
4 changes: 2 additions & 2 deletions modules/nf-core/bakta/baktadbdownload/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ process BAKTA_BAKTADBDOWNLOAD {

conda "${moduleDir}/environment.yml"
container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/bakta:1.11.4--pyhdfd78af_0'
: 'quay.io/biocontainers/bakta:1.11.4--pyhdfd78af_0'}"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/50/50b75335f6394ae83fd05f364db27ee2eb75f4170e3525bb2aea47ad717a9e64/data'
: 'community.wave.seqera.io/library/bakta_diamond:7830b94718da4f96'}"

output:
path "db*", emit: db
Expand Down
16 changes: 8 additions & 8 deletions modules/nf-core/bakta/baktadbdownload/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -6,15 +6,15 @@
[
"BAKTA_BAKTADBDOWNLOAD",
"bakta",
"1.11.4"
"1.12.0"
]
]
}
],
"timestamp": "2026-03-17T21:23:17.513160347",
"timestamp": "2026-06-18T14:36:06.696663407",
"meta": {
"nf-test": "0.9.4",
"nextflow": "26.02.0"
"nf-test": "0.9.5",
"nextflow": "26.04.3"
}
},
"Bakta database download - stub": {
Expand All @@ -30,15 +30,15 @@
[
"BAKTA_BAKTADBDOWNLOAD",
"bakta",
"1.11.4"
"1.12.0"
]
]
}
],
"timestamp": "2026-03-18T10:36:34.397679686",
"timestamp": "2026-06-18T14:36:14.006059546",
"meta": {
"nf-test": "0.9.4",
"nextflow": "26.02.0"
"nf-test": "0.9.5",
"nextflow": "26.04.3"
}
}
}
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