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Update KRAKENUNIQ_BUILD to make input taxonomy files properly compliant #11304

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Merged
jfy133 merged 3 commits into from
Apr 26, 2026
Merged

Update KRAKENUNIQ_BUILD to make input taxonomy files properly compliant #11304

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6bbe812
Make input taxonomy files properly compliant
jfy133 Apr 25, 2026
2581594
Update snapshot to include the taxonomy files
jfy133 Apr 25, 2026
5112744
Topics conversion for all krakenuniq modules for linting
jfy133 Apr 25, 2026
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14 changes: 2 additions & 12 deletions modules/nf-core/krakenuniq/build/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,12 @@ process KRAKENUNIQ_BUILD {
: 'quay.io/biocontainers/krakenuniq:1.0.4--pl5321h6dccd9a_2'}"

input:
tuple val(meta), path(custom_library_dir, stageAs: "library/*"), path(custom_taxonomy_dir, stageAs: "taxonomy"), path(custom_seqid2taxid)
tuple val(meta), path(custom_library_dir, stageAs: "library/*"), path(custom_taxonomy_dir, stageAs: "taxonomy/*"), path(custom_seqid2taxid, stageAs: 'seqid2taxid.map')
val keep_intermediate

output:
tuple val(meta), path("${prefix}/"), emit: db
path "versions.yml", emit: versions
tuple val("${task.process}"), val('krakenuniq'), eval("krakenuniq --version | sed '1!d;s/KrakenUniq version //'"), emit: versions_krakenuniq, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -33,11 +33,6 @@ process KRAKENUNIQ_BUILD {
--db ${prefix}

${run_cleanup}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
END_VERSIONS
"""

stub:
Expand All @@ -52,10 +47,5 @@ process KRAKENUNIQ_BUILD {
touch ${prefix}/database.kdb.counts
touch ${prefix}/database.kraken.tsv
touch ${prefix}/database.report.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
END_VERSIONS
"""
}
37 changes: 26 additions & 11 deletions modules/nf-core/krakenuniq/build/meta.yml
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Expand Up @@ -14,7 +14,8 @@ tools:
documentation: https://github.com/fbreitwieser/krakenuniq
tool_dev_url: https://github.com/fbreitwieser/krakenuniq
doi: 10.1186/s13059-018-1568-0
licence: ["MIT"]
licence:
- "MIT"
identifier: biotools:KrakenUniq
input:
- - meta:
Expand All @@ -24,12 +25,13 @@ input:
e.g. [ id:'test', single_end:false ]
- custom_library_dir:
type: directory
description: Optional directory containing custom fasta files for database build
description: Optional directory containing custom fasta files for database
build
pattern: "*"
- custom_taxonomy_dir:
type: directory
description: Optional directory containing custom taxonomy files for database
build
description: Optional directory containing custom taxonomy files for
database build
pattern: "*"
- custom_seqid2taxid:
type: file
Expand All @@ -39,7 +41,6 @@ input:
type: boolean
description: "Keep intermediate files that are not used by the database itself"
pattern: true|false

output:
db:
- - meta:
Expand All @@ -51,13 +52,27 @@ output:
type: directory
description: Directory containing KrakenUniq database
pattern: "*/"
versions_krakenuniq:
- - ${task.process}:
type: string
description: The name of the process
- krakenuniq:
type: string
description: The name of the tool
- krakenuniq --version | sed '1!d;s/KrakenUniq version //':
type: eval
description: The expression to obtain 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 name of the process
- krakenuniq:
type: string
description: The name of the tool
- krakenuniq --version | sed '1!d;s/KrakenUniq version //':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@jfy133"
maintainers:
Expand Down
4 changes: 2 additions & 2 deletions modules/nf-core/krakenuniq/build/tests/main.nf.test
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Expand Up @@ -55,7 +55,7 @@ nextflow_process {
{ assert snapshot(
stablefiles.sort(),
unstablefiles.sort(),
process.out.versions
process.out.findAll { key, val -> key.startsWith('versions') }
).match()
}
)
Expand Down Expand Up @@ -96,7 +96,7 @@ test("sarscov2 - fasta - nocleanup") {
{ assert snapshot(
stablefiles.sort(),
unstablefiles.sort(),
process.out.versions
process.out.findAll { key, val -> key.startsWith('versions') }
).match()
}
)
Expand Down
78 changes: 55 additions & 23 deletions modules/nf-core/krakenuniq/build/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,11 @@
]
],
"1": [
"versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325"
[
"KRAKENUNIQ_BUILD",
"krakenuniq",
"1.0.4"
]
],
"db": [
[
Expand All @@ -37,16 +41,20 @@
]
]
],
"versions": [
"versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325"
"versions_krakenuniq": [
[
"KRAKENUNIQ_BUILD",
"krakenuniq",
"1.0.4"
]
]
}
],
"timestamp": "2026-04-25T13:34:52.419463205",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-03-06T09:45:24.957949175"
"nf-test": "0.9.5",
"nextflow": "25.10.4"
}
},
"sarscov2 - fasta - nocleanup": {
"content": [
Expand All @@ -60,25 +68,43 @@
"library-files.txt:md5,8a9817d2de8465eb436aa3aa8696a717",
"genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
"seqid2taxid.map:md5,fe738f2333d57dde0db32239c04a93b8",
"taxDB:md5,1accaa141403e1fd5be9c79d1e5872b4"
"taxDB:md5,2a6c6234f8f4edba2b94ec75ea9f1b4c",
"citations.dmp:md5,7b2e5d0fbea3da110c4a0e3bb7c3720d",
"division.dmp:md5,f93fc4c838fdaa4b8923f003e8c11712",
"gc.prt:md5,accfbf13bca0899e7ba9849195af241a",
"gencode.dmp:md5,a5f39fc7a6608775d4c62a96cf1d170c",
"images.dmp:md5,3855c67cfa06ef8ae713cab73f009e3d",
"merged.dmp:md5,5e78eb1c4a235889458ef9f83a64e81e",
"readme.txt:md5,051060a90b7b89ad8e0fa33fe280211c"
],
[
"database-build.log",
"database-build.log",
"database.report.tsv",
"delnodes.dmp",
"names.dmp",
"names.dmp",
"nodes.dmp",
"nodes.dmp",
"taxdump.tar.gz",
"taxdump.tar.gz",
"timestamp"
],
[
"versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325"
]
{
"versions_krakenuniq": [
[
"KRAKENUNIQ_BUILD",
"krakenuniq",
"1.0.4"
]
]
}
],
"timestamp": "2026-04-25T13:34:38.850675715",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-03-06T09:49:11.884850884"
"nf-test": "0.9.5",
"nextflow": "25.10.4"
}
},
"sarscov2 - fasta": {
"content": [
Expand All @@ -87,19 +113,25 @@
"database.kdb:md5,46542be19979e867075f9e455a314e00",
"database.kdb.counts:md5,a82149480a435210ec1e870f06b6cdb3",
"database0.kdb:md5,46542be19979e867075f9e455a314e00",
"taxDB:md5,1accaa141403e1fd5be9c79d1e5872b4"
"taxDB:md5,2a6c6234f8f4edba2b94ec75ea9f1b4c"
],
[

],
[
"versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325"
]
{
"versions_krakenuniq": [
[
"KRAKENUNIQ_BUILD",
"krakenuniq",
"1.0.4"
]
]
}
],
"timestamp": "2026-04-25T13:33:43.689590026",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-03-06T09:48:27.136442441"
"nf-test": "0.9.5",
"nextflow": "25.10.4"
}
}
}
12 changes: 1 addition & 11 deletions modules/nf-core/krakenuniq/download/main.nf
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Expand Up @@ -11,7 +11,7 @@ process KRAKENUNIQ_DOWNLOAD {

output:
path "${pattern}/", emit: output
path "versions.yml", emit: versions
tuple val("${task.process}"), val('krakenuniq'), eval("krakenuniq --version | sed '1!d;s/KrakenUniq version //'"), emit: versions_krakenuniq, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -24,20 +24,10 @@ process KRAKENUNIQ_DOWNLOAD {
-o ${pattern}/ \\
${pattern} \\
${args}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
END_VERSIONS
"""

stub:
"""
mkdir ${pattern}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
END_VERSIONS
"""
}
37 changes: 26 additions & 11 deletions modules/nf-core/krakenuniq/download/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,26 +14,41 @@ tools:
documentation: https://github.com/fbreitwieser/krakenuniq
tool_dev_url: https://github.com/fbreitwieser/krakenuniq
doi: 10.1186/s13059-018-1568-0
licence: ["MIT"]
licence:
- "MIT"
identifier: biotools:KrakenUniq
input:
- pattern:
type: string
description: Pattern indicating what type of NCBI data to download. See KrakenUniq
documnation for possibilities.
description: Pattern indicating what type of NCBI data to download. See
KrakenUniq documnation for possibilities.
output:
output:
- ${pattern}/:
type: directory
description: Directory containing downloaded data with directory naming being
the user provided pattern.
description: Directory containing downloaded data with directory naming
being the user provided pattern.
versions_krakenuniq:
- - ${task.process}:
type: string
description: The name of the process
- krakenuniq:
type: string
description: The name of the tool
- krakenuniq --version | sed '1!d;s/KrakenUniq version //':
type: eval
description: The expression to obtain 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 name of the process
- krakenuniq:
type: string
description: The name of the tool
- krakenuniq --version | sed '1!d;s/KrakenUniq version //':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@jfy133"
maintainers:
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/krakenuniq/download/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ nextflow_process {
{ assert snapshot(
stablefiles.sort(),
unstablefiles.sort(),
process.out.versions
process.out.findAll { key, val -> key.startsWith('versions') }
).match()
}
)
Expand Down
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