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Merged
SPPearce merged 7 commits into from
May 22, 2024
Merged

Added nf-test for gatk4/intervallisttools #5672

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7ebf7a4
Added nf-test for gatk4/intervallisttools
KamilMaliszArdigen May 22, 2024
c612e29
Merge branch 'master' into feat_add_nf-test_gatk4/intervallisttools
KamilMaliszArdigen May 22, 2024
436adca
Merge branch 'master' into feat_add_nf-test_gatk4/intervallisttools
KamilMaliszArdigen May 22, 2024
0bd7427
Update modules/nf-core/gatk4/intervallisttools/tests/main.nf.test
KamilMaliszArdigen May 22, 2024
0bd3e35
Added nf-test stub for gatk4/intervallisttools
KamilMaliszArdigen May 22, 2024
16c90b3
Updated snap nf-test stub for gatk4/intervallisttools
KamilMaliszArdigen May 22, 2024
2bb0a5d
Merge branch 'master' into feat_add_nf-test_gatk4/intervallisttools
SPPearce May 22, 2024
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72 changes: 72 additions & 0 deletions modules/nf-core/gatk4/intervallisttools/tests/main.nf.test
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nextflow_process {

name "Test Process GATK4_INTERVALLISTTOOLS"
script "../main.nf"
process "GATK4_INTERVALLISTTOOLS"
config "./nextflow.config"

tag "modules"
tag "modules_nfcore"
tag "gatk4"
tag "gatk4/bedtointervallist"
tag "gatk4/intervallisttools"

setup {
run("GATK4_BEDTOINTERVALLIST") {
script "../../bedtointervallist/main.nf"
process {
"""
input[0] = [
[ id:'test' ], // meta map
[file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)]
]
input[1] = [
[ id:'dict' ], // meta map
[file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
]
"""
}
}
}

test("test_gatk4_intervallisttools") {

when {
process {
"""
input[0] = GATK4_BEDTOINTERVALLIST.out.interval_list
"""
}
}

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

}

test("test_gatk4_intervallisttools -stub") {

options "-stub"

when {
process {
"""
input[0] = GATK4_BEDTOINTERVALLIST.out.interval_list
"""
}
}

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

}

}
88 changes: 88 additions & 0 deletions modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap
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{
"test_gatk4_intervallisttools": {
"content": [
{
"0": [
[
{
"id": "test"
},
[
"1scattered.interval_list:md5,64f6665f9fbd257e4a300ec602f4e995",
"2scattered.interval_list:md5,f515c3da0c6accfd8e7dc33df50855c5",
"3scattered.interval_list:md5,7a918e8c9211b54334587793e8cbae53",
"4scattered.interval_list:md5,1b93105227a7dc81f07101a1efd31498"
]
]
],
"1": [
"versions.yml:md5,ff682cc9ad70d65a80280df57b316b03"
],
"interval_list": [
[
{
"id": "test"
},
[
"1scattered.interval_list:md5,64f6665f9fbd257e4a300ec602f4e995",
"2scattered.interval_list:md5,f515c3da0c6accfd8e7dc33df50855c5",
"3scattered.interval_list:md5,7a918e8c9211b54334587793e8cbae53",
"4scattered.interval_list:md5,1b93105227a7dc81f07101a1efd31498"
]
]
],
"versions": [
"versions.yml:md5,ff682cc9ad70d65a80280df57b316b03"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.04.2"
},
"timestamp": "2024-05-22T21:26:22.252885"
},
"test_gatk4_intervallisttools -stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
[
"1scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
"2scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
"3scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
"4scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"1": [
"versions.yml:md5,ff682cc9ad70d65a80280df57b316b03"
],
"interval_list": [
[
{
"id": "test"
},
[
"1scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
"2scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
"3scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
"4scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"versions": [
"versions.yml:md5,ff682cc9ad70d65a80280df57b316b03"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.04.2"
},
"timestamp": "2024-05-22T22:15:11.772344"
}
}
4 changes: 0 additions & 4 deletions ...e/gatk4/intervallisttools/nextflow.config → ...4/intervallisttools/tests/nextflow.config
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@@ -1,9 +1,5 @@
process {

publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

withName: GATK4_INTERVALLISTTOOLS {
ext.args = '--SCATTER_COUNT 6 --SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW --UNIQUE true --SORT true'
}

}
2 changes: 2 additions & 0 deletions modules/nf-core/gatk4/intervallisttools/tests/tags.yml
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@@ -0,0 +1,2 @@
gatk4/intervallisttools:
- "modules/nf-core/gatk4/intervallisttools/**"
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Expand Up @@ -618,9 +618,6 @@ gatk4/germlinecnvcaller:
gatk4/intervallisttobed:
- modules/nf-core/gatk4/intervallisttobed/**
- tests/modules/nf-core/gatk4/intervallisttobed/**
gatk4/intervallisttools:
- modules/nf-core/gatk4/intervallisttools/**
- tests/modules/nf-core/gatk4/intervallisttools/**
gatk4/learnreadorientationmodel:
- modules/nf-core/gatk4/learnreadorientationmodel/**
- tests/modules/nf-core/gatk4/learnreadorientationmodel/**
Expand Down
19 changes: 0 additions & 19 deletions tests/modules/nf-core/gatk4/intervallisttools/main.nf
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17 changes: 0 additions & 17 deletions tests/modules/nf-core/gatk4/intervallisttools/test.yml
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