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Added nf-test for krona/ktimporttaxonomy #7365

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Added nf-test for krona/ktimporttaxonomy #7365

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50a50b8
Added agat/agatconvertbed2gff
GallVp Jan 15, 2025
9b7a89b
Added nf-test for krona/ktimporttaxonomy
GallVp Jan 25, 2025
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7 changes: 7 additions & 0 deletions modules/nf-core/agat/agatconvertbed2gff/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::agat=1.4.2"
45 changes: 45 additions & 0 deletions modules/nf-core/agat/agatconvertbed2gff/main.nf
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process AGAT_AGATCONVERTBED2GFF {
tag "$meta.id"
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/agat:1.4.0--pl5321hdfd78af_0' :
'biocontainers/agat:1.4.0--pl5321hdfd78af_0' }"

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

output:
tuple val(meta), path("*.gff") , emit: gff
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
agat_convert_bed2gff.pl \\
--bed $bed \\
--output ${prefix}.gff \\
$args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
agat: \$(agat_convert_bed2gff.pl --help | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.gff

cat <<-END_VERSIONS > versions.yml
"${task.process}":
agat: \$(agat_convert_bed2gff.pl --help | sed -n 's/.*(AGAT) - Version: \\(.*\\) .*/\\1/p')
END_VERSIONS
"""
}
49 changes: 49 additions & 0 deletions modules/nf-core/agat/agatconvertbed2gff/meta.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: agat_agatconvertbed2gff
description: |
Takes a bed12 file and converts to a GFF3 file
keywords:
- genome
- bed
- gff
- conversion
tools:
- agat:
description: "AGAT is a toolkit for manipulation and getting information from
GFF/GTF files"
homepage: "https://github.com/NBISweden/AGAT"
documentation: "https://agat.readthedocs.io/"
tool_dev_url: "https://github.com/NBISweden/AGAT"
doi: "10.5281/zenodo.3552717"
licence: ["GPL v3"]
identifier: biotools:AGAT
input:
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Input bed12 file
pattern: "*.bed"
output:
- gff:
- meta:
type: map
description: Groovy Map containing sample information
- "*.gff":
type: file
description: Output GFF3 file
pattern: "*.{gff}"
- versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"

authors:
- "@GallVp"
maintainers:
- "@GallVp"
58 changes: 58 additions & 0 deletions modules/nf-core/agat/agatconvertbed2gff/tests/main.nf.test
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nextflow_process {

name "Test Process AGAT_AGATCONVERTBED2GFF"
script "../main.nf"
process "AGAT_AGATCONVERTBED2GFF"

tag "modules"
tag "modules_nfcore"
tag "agat"
tag "agat/agatconvertbed2gff"

test("sarscov2 - bed12") {

when {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed12', checkIfExists: true)
]
"""
}
}

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

}

test("sarscov2 - bam - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed12', checkIfExists: true)
]
"""
}
}

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

}

}
70 changes: 70 additions & 0 deletions modules/nf-core/agat/agatconvertbed2gff/tests/main.nf.test.snap
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{
"sarscov2 - bam - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,c43855fa732ead39246ba2aa2b044e1c"
],
"gff": [
[
{
"id": "test",
"single_end": false
},
"test.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,c43855fa732ead39246ba2aa2b044e1c"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-15T13:31:55.362837"
},
"sarscov2 - bed12": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.gff:md5,4e5a23a6babac6d5b1bcfa06c5b12518"
]
],
"1": [
"versions.yml:md5,c43855fa732ead39246ba2aa2b044e1c"
],
"gff": [
[
{
"id": "test"
},
"test.gff:md5,4e5a23a6babac6d5b1bcfa06c5b12518"
]
],
"versions": [
"versions.yml:md5,c43855fa732ead39246ba2aa2b044e1c"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-15T13:31:49.570205"
}
}
1 change: 0 additions & 1 deletion modules/nf-core/krona/ktimporttaxonomy/main.nf
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Expand Up @@ -40,7 +40,6 @@ process KRONA_KTIMPORTTAXONOMY {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '2.8.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
Expand Down
100 changes: 80 additions & 20 deletions modules/nf-core/krona/ktimporttaxonomy/tests/main.nf.test
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nextflow_process {

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

Expand All @@ -9,53 +10,112 @@ nextflow_process {
tag "krona"
tag "krona/ktimporttaxonomy"

test ("sarscov2 - metagenome - kraken report") {


test("test_krona_ktimporttaxonomy_reads") {

when {
params {
module_args = '-t 3'
}
process {
"""
input[0] = Channel.of([
[id: 'test'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true)
])
input[1] = Channel.of([
file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/krona_taxonomy.tab', checkIfExists: true)
])
input[0] = [
[id:'test',single_end:false],// meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.reads.txt', checkIfExists: true)
]
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/krona_taxonomy.tab', checkIfExists: true)
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.html[0][1]).text.contains('Severe acute respiratory syndrome-related coronavirus'),
process.out.versions
).match()
}
)
}
}


test("test_krona_ktimporttaxonomy_report") {

when {
params {
module_args = '-m 3 -t 5'
}
process {
"""
input[0] = [
[id:'test',single_end:false],// meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true)
]
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/krona_taxonomy.tab', checkIfExists: true)
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot ( process.out.versions ).match() },
{ assert file(process.out.html.get(0).get(1)).exists() }
{ assert snapshot(
file(process.out.html[0][1]).text.contains('Severe acute respiratory syndrome-related coronavirus'),
process.out.versions
).match()
}
)
}
}

test ("sarscov2 - metagenome - kraken report - stub") {

test("test_krona_ktimporttaxonomy_reads -- stub") {
options '-stub'
when {
params {
module_args = '-t 3'
}
process {
"""
input[0] = Channel.of([
[id: 'test'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true)
])
input[1] = Channel.of([
file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/krona_taxonomy.tab', checkIfExists: true)
])
input[0] = [
[id:'test',single_end:false],// meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.reads.txt', checkIfExists: true)
]
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/krona_taxonomy.tab', checkIfExists: true)
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}


test("test_krona_ktimporttaxonomy_report -- stub") {
options '-stub'
when {
params {
module_args = '-m 3 -t 5'
}
process {
"""
input[0] = [
[id:'test',single_end:false],// meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/test_1.kraken2.report.txt', checkIfExists: true)
]
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/krona_taxonomy.tab', checkIfExists: true)
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out).match() }
)
}
}
}
}
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