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Migrate ATAQV/MKARV to nf-test #7893

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Merged
SPPearce merged 1 commit into from
Mar 24, 2025
Merged

Migrate ATAQV/MKARV to nf-test #7893

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11 changes: 11 additions & 0 deletions modules/nf-core/ataqv/mkarv/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -32,4 +32,15 @@ process ATAQV_MKARV {
ataqv: \$( ataqv --version )
END_VERSIONS
"""

stub:
"""
mkdir -p html
touch html/index.html
cat <<-END_VERSIONS > versions.yml
"${task.process}":
# mkarv: \$( mkarv --version ) # Use this when version string has been fixed
ataqv: \$( ataqv --version )
END_VERSIONS
"""
}
79 changes: 79 additions & 0 deletions modules/nf-core/ataqv/mkarv/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -0,0 +1,79 @@
nextflow_process {

name "Test Process ATAQV_MKARV"

script "../main.nf"
process "ATAQV_MKARV"

tag "modules"
tag "modules_nfcore"
tag "ataqv"
tag "ataqv/ataqv"
tag "ataqv/mkarv"

setup {
run("ATAQV_ATAQV") {
script "../../ataqv/main.nf"

process {
"""
input[0] = [
[id:'test',single_end:false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam',checkIfExists:true),
[],
[]
]
input[1] = 'human'
input[2] = ''
input[3] = []
input[4] = []
input[5] = []
"""
}
}
}

test("test_ataqv_mkarv") {
when {
params {
module_args = ''
}
process {
"""
input[0] = ATAQV_ATAQV.out.json.collect{it[1]}
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}

test("test_ataqv_mkarv - stub") {

options '-stub'

when {
params {
module_args = ''
}
process {
"""
input[0] = ATAQV_ATAQV.out.json.collect{it[1]}
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
process.out.versions.collect{path(it).yaml}
).match() }
)
}
}
}
123 changes: 123 additions & 0 deletions modules/nf-core/ataqv/mkarv/tests/main.nf.test.snap
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@@ -0,0 +1,123 @@
{
"test_ataqv_mkarv - stub": {
"content": [
{
"0": [
[
"index.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,f0f11bfec7e5fc5776c4af08db94655f"
],
"html": [
[
"index.html:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,f0f11bfec7e5fc5776c4af08db94655f"
]
},
[
{
"ATAQV_MKARV": {
"ataqv": "1.3.1"
}
}
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-03-23T19:29:21.09850825"
},
"test_ataqv_mkarv": {
"content": [
{
"0": [
[
[
"ataqv.css:md5,7bb9e18974018dd29bdc12a46a6d6d65",
"datatables.buttons.min.css:md5,675306abc9d3239314f2c66c0e22ef7a",
"datatables.fontawesome.css:md5,716d7a3edd2c75e712b1ffe26f12a861",
"datatables.min.css:md5,00ef3e39d9302618395ab189ec8bcd9f",
"font-awesome.min.css:md5,89916fa773ce96569604016ef25cab50",
"normalize.css:md5,40d20cc85100840580df4346bb99d7ed"
],
[
"1.json.gz:md5,7c01e4f0136404e6db2328485d68d154"
],
[
"FontAwesome.otf:md5,9ccfa32dd4cd1b8e83f68899d85bd5e6",
"fontawesome-webfont.eot:md5,404a525502f8e5ba7e93b9f02d9e83a9",
"fontawesome-webfont.svg:md5,bae4a87c1e5dff40baa3f49d52f5347a",
"fontawesome-webfont.ttf:md5,fb650aaf10736ffb9c4173079616bf01",
"fontawesome-webfont.woff:md5,891e3f340c1126b4c7c142e5f6e86816",
"fontawesome-webfont.woff2:md5,926c93d201fe51c8f351e858468980c3",
"sourcesanspro-regular.woff:md5,f7bd788f18b8c4bb93dd37d140348e1e",
"sourcesanspro-regularit.woff:md5,c3638b17f4fd76dae12fe2ae14571e57",
"sourcesanspro-semibold.woff:md5,e7fc8925d9364e9d177d9e1d08bb1855",
"sourcesanspro-semiboldit.woff:md5,f1d255aa459786dfc6aa2e488ac01245"
],
"index.html:md5,bf7747be761e56ad7c54c842ac88461a",
[
"ataqv.js:md5,feb291b7839e9e43ed304565e3a605d9",
"configuration.js:md5,073bc07f1371e28a97098f8b10469ae4",
"d3.min.js:md5,db69fb2626a71a286ee772d673138aca",
"datatables.min.js:md5,e369b872620dadb05e4eb555b81f9112",
"jszip.min.js:md5,09e492cb492ffa75484bbe10f1f721d1"
]
]
],
"1": [
"versions.yml:md5,f0f11bfec7e5fc5776c4af08db94655f"
],
"html": [
[
[
"ataqv.css:md5,7bb9e18974018dd29bdc12a46a6d6d65",
"datatables.buttons.min.css:md5,675306abc9d3239314f2c66c0e22ef7a",
"datatables.fontawesome.css:md5,716d7a3edd2c75e712b1ffe26f12a861",
"datatables.min.css:md5,00ef3e39d9302618395ab189ec8bcd9f",
"font-awesome.min.css:md5,89916fa773ce96569604016ef25cab50",
"normalize.css:md5,40d20cc85100840580df4346bb99d7ed"
],
[
"1.json.gz:md5,7c01e4f0136404e6db2328485d68d154"
],
[
"FontAwesome.otf:md5,9ccfa32dd4cd1b8e83f68899d85bd5e6",
"fontawesome-webfont.eot:md5,404a525502f8e5ba7e93b9f02d9e83a9",
"fontawesome-webfont.svg:md5,bae4a87c1e5dff40baa3f49d52f5347a",
"fontawesome-webfont.ttf:md5,fb650aaf10736ffb9c4173079616bf01",
"fontawesome-webfont.woff:md5,891e3f340c1126b4c7c142e5f6e86816",
"fontawesome-webfont.woff2:md5,926c93d201fe51c8f351e858468980c3",
"sourcesanspro-regular.woff:md5,f7bd788f18b8c4bb93dd37d140348e1e",
"sourcesanspro-regularit.woff:md5,c3638b17f4fd76dae12fe2ae14571e57",
"sourcesanspro-semibold.woff:md5,e7fc8925d9364e9d177d9e1d08bb1855",
"sourcesanspro-semiboldit.woff:md5,f1d255aa459786dfc6aa2e488ac01245"
],
"index.html:md5,bf7747be761e56ad7c54c842ac88461a",
[
"ataqv.js:md5,feb291b7839e9e43ed304565e3a605d9",
"configuration.js:md5,073bc07f1371e28a97098f8b10469ae4",
"d3.min.js:md5,db69fb2626a71a286ee772d673138aca",
"datatables.min.js:md5,e369b872620dadb05e4eb555b81f9112",
"jszip.min.js:md5,09e492cb492ffa75484bbe10f1f721d1"
]
]
],
"versions": [
"versions.yml:md5,f0f11bfec7e5fc5776c4af08db94655f"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-03-23T19:24:40.06356836"
}
}
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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@@ -1,6 +1,3 @@
ataqv/mkarv:
- modules/nf-core/ataqv/mkarv/**
- tests/modules/nf-core/ataqv/mkarv/**
authentict/deam2cont:
- modules/nf-core/authentict/deam2cont/**
- tests/modules/nf-core/authentict/deam2cont/**
Expand Down
19 changes: 0 additions & 19 deletions tests/modules/nf-core/ataqv/mkarv/main.nf
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5 changes: 0 additions & 5 deletions tests/modules/nf-core/ataqv/mkarv/nextflow.config
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55 changes: 0 additions & 55 deletions tests/modules/nf-core/ataqv/mkarv/test.yml
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