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Update to topic metamaps/* #12246

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a6e44ac
Update to topic
LouisLeNezet Jul 6, 2026
3d0d224
[automated] Fix code linting
nf-core-bot Jul 6, 2026
e116f29
Merge branch 'master' into metamaps
itrujnara Jul 6, 2026
c2b693b
Revert "[automated] Fix code linting"
LouisLeNezet Jul 6, 2026
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12 changes: 1 addition & 11 deletions modules/nf-core/metamaps/classify/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ process METAMAPS_CLASSIFY {
tuple val(meta), path("*classification_res.EM.contigCoverage") , emit: contig_coverage
tuple val(meta), path("*classification_res.EM.lengthAndIdentitiesPerMappingUnit") , emit: length_and_id
tuple val(meta), path("*classification_res.EM.reads2Taxon.krona") , emit: krona
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('metamaps'), eval("metamaps | sed -n 's/.*MetaMaps v //p'"), emit: versions_metamaps, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -34,11 +34,6 @@ process METAMAPS_CLASSIFY {
--mappings ${classification_res} \\
--threads ${task.cpus} \\
--DB ${database_folder}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
metamaps: \$(metamaps | sed -n 2p | sed 's/^.*MetaMaps v //')
END_VERSIONS
"""

stub:
Expand All @@ -51,11 +46,6 @@ process METAMAPS_CLASSIFY {
touch ${prefix}_classification_res.EM.contigCoverage
touch ${prefix}_classification_res.EM.lengthAndIdentitiesPerMappingUnit
touch ${prefix}_classification_res.EM.reads2Taxon.krona

cat <<-END_VERSIONS > versions.yml
"${task.process}":
metamaps: \$(metamaps | sed -n 2p | sed 's/^.*MetaMaps v //')
END_VERSIONS
"""

}
31 changes: 24 additions & 7 deletions modules/nf-core/metamaps/classify/meta.yml
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Expand Up @@ -12,7 +12,8 @@ tools:
documentation: https://github.com/DiltheyLab/MetaMaps/blob/master/README.md
tool_dev_url: https://github.com/DiltheyLab/MetaMaps
doi: "10.1038/s41467-019-10934-2"
licence: ["Public Domain"]
licence:
- "Public Domain"
identifier: biotools:metamaps

input:
Expand Down Expand Up @@ -123,13 +124,29 @@ output:
description: Taxon ID assignment of reads in Krona format
pattern: "*.{classification_res.EM.reads2Taxon.krona}"
ontologies: []
versions_metamaps:
- - ${task.process}:
type: string
description: The name of the process
- metamaps:
type: string
description: The name of the tool
- metamaps | sed -n 's/.*MetaMaps v //p':
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
- metamaps:
type: string
description: The name of the tool
- metamaps | sed -n 's/.*MetaMaps v //p':
type: eval
description: The expression to obtain the version of the tool

authors:
- "@henningonsbring"
- "@sofstam"
104 changes: 35 additions & 69 deletions modules/nf-core/metamaps/classify/tests/main.nf.test
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Expand Up @@ -2,6 +2,7 @@ nextflow_process {

name "Test Process METAMAPS_CLASSIFY"
script "../main.nf"
config "./nextflow.config"
process "METAMAPS_CLASSIFY"

tag "modules"
Expand All @@ -11,52 +12,49 @@ nextflow_process {
tag "metamaps/classify"
tag "untar"

test("sarscov2_nanopore_classify") {
setup {
run("UNTAR") {
config "./nextflow.config"
script "../../../untar/main.nf"
process {
"""
input[0] = [
[],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/metamaps_db.tar.gz', checkIfExists: true)
]
"""
}
setup {
run("UNTAR") {
script "../../../untar/main.nf"
process {
"""
input[0] = [
[],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/metamaps_db.tar.gz', checkIfExists: true)
]
"""
}
run("METAMAPS_MAPDIRECTLY") {
script "../../../metamaps/mapdirectly/main.nf"
process {
"""
input[0] = [
[ id:'test', single_end:true ], // meta map
}
run("METAMAPS_MAPDIRECTLY") {
script "../../../metamaps/mapdirectly/main.nf"
process {
"""
input[0] = [
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
]
input[1] = UNTAR.out.untar.map{ it[1] }
"""
}
]
input[1] = UNTAR.out.untar.map{ it[1] }
"""
}
}
}

test("sarscov2_nanopore_classify") {
when {
process {
"""
classification_folder = METAMAPS_MAPDIRECTLY.out.classification_res
.join(METAMAPS_MAPDIRECTLY.out.meta_file)
.join(METAMAPS_MAPDIRECTLY.out.meta_unmappedreadsLengths)
.join(METAMAPS_MAPDIRECTLY.out.para_file)
input[0] = classification_folder
input[0] = METAMAPS_MAPDIRECTLY.out.classification_res
.join(METAMAPS_MAPDIRECTLY.out.meta_file)
.join(METAMAPS_MAPDIRECTLY.out.meta_unmappedreadsLengths)
.join(METAMAPS_MAPDIRECTLY.out.para_file)
input[1] = UNTAR.out.untar.map{ it[1] }
"""
}
}



then {
assertAll(
assertAll(
{ assert process.success },
{ assert snapshot ( sanitizeOutput(process.out) ).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand All @@ -66,55 +64,23 @@ nextflow_process {

options "-stub"

setup {
run("UNTAR") {
config "./nextflow.config"
script "../../../untar/main.nf"
process {
"""
input[0] = [
[],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/metamaps_db.tar.gz', checkIfExists: true)
]
"""
}
}
run("METAMAPS_MAPDIRECTLY") {
script "../../../metamaps/mapdirectly/main.nf"
process {
"""
input[0] = [
[ id:'test', single_end:true ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
]
input[1] = UNTAR.out.untar.map{ it[1] }
"""
}
}
}

when {
process {
"""
classification_folder = METAMAPS_MAPDIRECTLY.out.classification_res
.join(METAMAPS_MAPDIRECTLY.out.meta_file)
.join(METAMAPS_MAPDIRECTLY.out.meta_unmappedreadsLengths)
.join(METAMAPS_MAPDIRECTLY.out.para_file)
input[0] = classification_folder
input[0] = METAMAPS_MAPDIRECTLY.out.classification_res
.join(METAMAPS_MAPDIRECTLY.out.meta_file)
.join(METAMAPS_MAPDIRECTLY.out.meta_unmappedreadsLengths)
.join(METAMAPS_MAPDIRECTLY.out.para_file)
input[1] = UNTAR.out.untar.map{ it[1] }
"""
}
}



then {
assertAll(
assertAll(
{ assert process.success },
{ assert snapshot ( sanitizeOutput(process.out) ).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

}


}
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