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Minia update #11065

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593cabb
topics, tests, log fixed. meta.yml needs update. lint needed
LiaOb21 Mar 26, 2026
591b76c
meta.yml updated
LiaOb21 Mar 27, 2026
5e7e737
docker and singularity for some reasons contained minia 3.2.5 despite…
LiaOb21 Mar 27, 2026
fa9df1b
[automated] Fix linting with Prettier
nf-core-bot Mar 27, 2026
2030686
fix singularity
LiaOb21 Mar 27, 2026
d0c86d0
Fix container URL for Minia process
LiaOb21 Mar 27, 2026
03f8e18
Merge branch 'master' into minia_update
LiaOb21 Mar 27, 2026
5f69b36
Sorry!
LiaOb21 Mar 27, 2026
858a708
Updating containers - sorry2
LiaOb21 Mar 27, 2026
9b1f2d3
Update modules/nf-core/minia/tests/main.nf.test
LiaOb21 Mar 27, 2026
97c6a6f
Update modules/nf-core/minia/main.nf
LiaOb21 Mar 27, 2026
368c250
snap update
LiaOb21 Mar 27, 2026
6303a99
Update modules/nf-core/minia/tests/main.nf.test
LiaOb21 Mar 30, 2026
df4d1ab
Update modules/nf-core/minia/meta.yml
LiaOb21 Mar 30, 2026
a969bcb
Update modules/nf-core/minia/meta.yml
LiaOb21 Mar 30, 2026
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37 changes: 18 additions & 19 deletions modules/nf-core/minia/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,17 +4,18 @@ process MINIA {

conda "${moduleDir}/environment.yml"
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@mashehu mashehu Mar 27, 2026

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can you update the version number in this file as well please

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' :
'biocontainers/minia:3.2.6--h9a82719_0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d1/d1127b772f97ea9d62cb853d174a8e82be7e8e8598933d49b2061cb0550e276f/data' :
'community.wave.seqera.io/library/minia:3.2.6--92bae1756baab1ef' }"

input:
tuple val(meta), path(reads)

output:
tuple val(meta), path('*.contigs.fa'), emit: contigs
tuple val(meta), path('*.unitigs.fa'), emit: unitigs
tuple val(meta), path('*.h5') , emit: h5
path "versions.yml" , emit: versions
tuple val(meta), path('*.contigs.fa.gz'), emit: contigs
tuple val(meta), path('*.unitigs.fa.gz'), emit: unitigs
tuple val(meta), path('*.h5') , emit: h5
tuple val(meta), path("*-minia.log") , emit: log
tuple val("${task.process}"), val("minia"), eval("minia -v | sed -n 's/Minia version //p'"), topic: versions, emit: versions_minia

when:
task.ext.when == null || task.ext.when
Expand All @@ -29,24 +30,22 @@ process MINIA {
$args \\
-nb-cores $task.cpus \\
-in input_files.txt \\
-out $prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
minia: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;')
END_VERSIONS
-out $prefix > ${prefix}-minia.log 2>&1

if [ -f ${prefix}.contigs.fa ]; then
gzip -cn ${prefix}.contigs.fa > ${prefix}.contigs.fa.gz
fi
if [ -f ${prefix}.unitigs.fa ]; then
gzip -cn ${prefix}.unitigs.fa > ${prefix}.unitigs.fa.gz
fi
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.contigs.fa
touch ${prefix}.unitigs.fa
echo "" | gzip > ${prefix}.contigs.fa.gz
echo "" | gzip > ${prefix}.unitigs.fa.gz
touch ${prefix}.h5

cat <<-END_VERSIONS > versions.yml
"${task.process}":
minia: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;')
END_VERSIONS
touch ${prefix}-minia.log
"""
}
70 changes: 50 additions & 20 deletions modules/nf-core/minia/meta.yml
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Expand Up @@ -11,60 +11,90 @@ tools:
a human genome on a desktop computer in a day. The output of Minia is a set of contigs.
homepage: https://github.com/GATB/minia
documentation: https://github.com/GATB/minia
licence: ["AGPL-3.0-or-later"]
licence:
- "AGPL-3.0-or-later"
identifier: biotools:minia
input:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
e.g. [ id:'test' ]
- reads:
type: file
description: Input reads in FastQ format
pattern: "*.{fastq.gz, fastq}"
ontologies: []
ontologies:
- edam: http://edamontology.org/format_1930 # FASTQ
output:
contigs:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- "*.contigs.fa":
e.g. [ id:'test' ]
- "*.contigs.fa.gz":
type: file
description: The assembled contigs
pattern: "*.contigs.fa"
ontologies: []
pattern: "*.contigs.fa.gz"
ontologies:
- edam: http://edamontology.org/format_3989
unitigs:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- "*.unitigs.fa":
e.g. [ id:'test' ]
- "*.unitigs.fa.gz":
type: file
description: The assembled unitigs
pattern: "*.unitigs.fa"
ontologies: []
pattern: "*.unitigs.fa.gz"
ontologies:
- edam: http://edamontology.org/format_3989
h5:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
e.g. [ id:'test' ]
- "*.h5":
type: file
description: Minia output h5 file
pattern: "*{.h5}"
description: Minia assembly graph in binary h5 format
pattern: "*.h5"
ontologies: []

log:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- "*-minia.log":
type: file
description: Minia assembly log file
pattern: "*-minia.log"
ontologies: []
versions_minia:
- - ${task.process}:
type: string
description: The name of the process
- minia:
type: string
description: The name of the tool
- minia -v | sed -n 's/Minia version //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
- minia:
type: string
description: The name of the tool
- minia -v | sed -n 's/Minia version //p':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@drpatelh"
- "@kevinmenden"
Expand Down
41 changes: 37 additions & 4 deletions modules/nf-core/minia/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,39 @@ nextflow_process {
tag "modules_nfcore"
tag "minia"

test("test-minia") {
test("sarscov2 - fastq - se") {

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true), ]
]

"""
}
}

then {
assertAll(
{ assert process.success },
{ assert path(process.out.contigs[0][1]).linesGzip.any { it.contains('AAA') } },
{ assert path(process.out.unitigs[0][1]).linesGzip.any { it.contains('CCC') } },
{ assert snapshot(
file(process.out.contigs[0][1]).name,
file(process.out.unitigs[0][1]).name,
file(process.out.h5[0][1]).name,
file(process.out.log[0][1]).name,
process.out.findAll { key, val -> key.startsWith('versions') }
).match()
}
)
}
}

test("sarscov2 - fastq - pe") {

when {
process {
Expand All @@ -29,13 +61,14 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert file(process.out.contigs[0][1]).text.contains('AAA') },
{ assert file(process.out.unitigs[0][1]).text.contains('CCC') },
{ assert path(process.out.contigs[0][1]).linesGzip.any { it.contains('AAA') } },
{ assert path(process.out.unitigs[0][1]).linesGzip.any { it.contains('CCC') } },
{ assert snapshot(
file(process.out.contigs[0][1]).name,
file(process.out.unitigs[0][1]).name,
file(process.out.h5[0][1]).name,
process.out.versions,
file(process.out.log[0][1]).name,
process.out.findAll { key, val -> key.startsWith('versions') },
).match()
}
)
Expand Down
85 changes: 68 additions & 17 deletions modules/nf-core/minia/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,18 +1,45 @@
{
"test-minia": {
"sarscov2 - fastq - se": {
"content": [
"test.contigs.fa",
"test.unitigs.fa",
"test.contigs.fa.gz",
"test.unitigs.fa.gz",
"test.h5",
"test-minia.log",
{
"versions_minia": [
[
"MINIA",
"minia",
"3.2.5"
]
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.4"
},
"timestamp": "2026-03-27T16:29:27.70699655"
},
"sarscov2 - fastq - pe": {
"content": [
"test.contigs.fa.gz",
"test.unitigs.fa.gz",
"test.h5",
"test-minia.log",
[
"versions.yml:md5,242f8593f9ee8955fb73580c78f30200"
[
"MINIA",
"minia",
"3.2.5"
]
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.3",
"nextflow": "25.10.4"
},
"timestamp": "2024-09-05T19:56:44.252673"
"timestamp": "2026-03-27T16:29:33.61312516"
},
"test-minia-stub": {
"content": [
Expand All @@ -22,15 +49,15 @@
{
"id": "test"
},
"test.contigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.contigs.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [
[
{
"id": "test"
},
"test.unitigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.unitigs.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"2": [
Expand All @@ -42,14 +69,26 @@
]
],
"3": [
"versions.yml:md5,242f8593f9ee8955fb73580c78f30200"
[
{
"id": "test"
},
"test-minia.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"4": [
[
"MINIA",
"minia",
"3.2.5"
]
],
"contigs": [
[
{
"id": "test"
},
"test.contigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.contigs.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"h5": [
Expand All @@ -60,23 +99,35 @@
"test.h5:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"log": [
[
{
"id": "test"
},
"test-minia.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"unitigs": [
[
{
"id": "test"
},
"test.unitigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.unitigs.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,242f8593f9ee8955fb73580c78f30200"
"versions_minia": [
[
"MINIA",
"minia",
"3.2.5"
]
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.3",
"nextflow": "25.10.4"
},
"timestamp": "2024-09-05T19:52:02.585904"
"timestamp": "2026-03-27T16:29:38.952052332"
}
}
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