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nf-test migration for universc #8478

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1 change: 1 addition & 0 deletions modules/nf-core/universc/main.nf
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Expand Up @@ -49,6 +49,7 @@ process UNIVERSC {
--per-cell-data \\
$args 1> _log 2> _err

mkdir sample-${meta.id}/outs/
# save log files
echo !! > sample-${meta.id}/outs/_invocation
cp _log sample-${meta.id}/outs/_log
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7 changes: 7 additions & 0 deletions modules/nf-core/universc/meta.yml
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Expand Up @@ -28,24 +28,31 @@ input:
type: file
description: FASTQ or FASTQ.GZ file, list of 2 files for paired-end data
pattern: "*.{fastq,fq,fastq.gz,fq.gz}"
ontologies:
- edam: http://edamontology.org/format_1930 # FASTQ
- - reference:
type: file
description: Reference genome file
ontologies: []
output:
- outs:
- meta:
type: file
description: Files containing the outputs of Cell Ranger
pattern: "sample-${meta.id}/outs/*"
ontologies: []
- sample-${meta.id}/outs/*:
type: file
description: Files containing the outputs of Cell Ranger
pattern: "sample-${meta.id}/outs/*"
ontologies: []
- versions:
- versions.yml:
type: file
description: File containing software version
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
authors:
- "@kbattenb"
- "@tomkellygenetics"
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88 changes: 88 additions & 0 deletions modules/nf-core/universc/tests/main.nf.test
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@@ -0,0 +1,88 @@
nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "cellranger"
tag "cellranger/mkgtf"
tag "cellranger/mkref"
tag "universc"

setup {
run("CELLRANGER_MKGTF") {
script "../../cellranger/mkgtf/main.nf"

process {
"""
input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf',checkIfExists:true)
"""
}
}

run("CELLRANGER_MKREF") {
script "../../cellranger/mkref/main.nf"

process {
"""
input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta',checkIfExists:true)
input[1] = CELLRANGER_MKGTF.out.gtf
input[2] = "homo_sapiens_chr22_reference"
"""
}
}
}

test("test_universc_10x") {

when {
params {
module_args = ''
}
process {
"""
input[0] = [[id:'123',technology:'10x',chemistry:'SC3Pv3',single_end:false,strandedness:'forward',samples:["test_10x"]],// meta map
[file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz',checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz',checkIfExists:true)
]
]
input[1] = CELLRANGER_MKREF.out.reference
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}


test("test_universc_10x -- stub") {
options '-stub'
when {
params {
module_args = ''
}
process {
"""
input[0] = [[id:'123',technology:'10x',chemistry:'SC3Pv3',single_end:false,strandedness:'forward',samples:["test_10x"]],// meta map
[file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz',checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz',checkIfExists:true)
]
]
input[1] = CELLRANGER_MKREF.out.reference
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
}
104 changes: 104 additions & 0 deletions modules/nf-core/universc/tests/main.nf.test.snap
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{
"test_universc_10x": {
"content": [
{
"0": [
[
{
"id": "123",
"technology": "10x",
"chemistry": "SC3Pv3",
"single_end": false,
"strandedness": "forward",
"samples": [
"test_10x"
]
},
[
"_err:md5,92544b75bfe4ad17becb3fa17b83dac9",
"_invocation:md5,adbbbc1027756be9fdeebabf979863e5",
"_log:md5,f4ab003ca08293ce9a80a2b2a3b25749"
]
]
],
"1": [
"versions.yml:md5,70bfcfea05b26a198a980e8b0eabb348"
],
"outs": [
[
{
"id": "123",
"technology": "10x",
"chemistry": "SC3Pv3",
"single_end": false,
"strandedness": "forward",
"samples": [
"test_10x"
]
},
[
"_err:md5,92544b75bfe4ad17becb3fa17b83dac9",
"_invocation:md5,adbbbc1027756be9fdeebabf979863e5",
"_log:md5,f4ab003ca08293ce9a80a2b2a3b25749"
]
]
],
"versions": [
"versions.yml:md5,70bfcfea05b26a198a980e8b0eabb348"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.2"
},
"timestamp": "2025-05-14T15:52:03.725881758"
},
"test_universc_10x -- stub": {
"content": [
{
"0": [
[
{
"id": "123",
"technology": "10x",
"chemistry": "SC3Pv3",
"single_end": false,
"strandedness": "forward",
"samples": [
"test_10x"
]
},
"fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,70bfcfea05b26a198a980e8b0eabb348"
],
"outs": [
[
{
"id": "123",
"technology": "10x",
"chemistry": "SC3Pv3",
"single_end": false,
"strandedness": "forward",
"samples": [
"test_10x"
]
},
"fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,70bfcfea05b26a198a980e8b0eabb348"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.2"
},
"timestamp": "2025-05-14T15:52:10.667692329"
}
}
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Expand Up @@ -146,9 +146,6 @@ ultra/align:
ultra/index:
- modules/nf-core/ultra/index/**
- tests/modules/nf-core/ultra/index/**
universc:
- modules/nf-core/universc/**
- tests/modules/nf-core/universc/**
varlociraptor/callvariants:
- modules/nf-core/varlociraptor/callvariants/**
- tests/modules/nf-core/varlociraptor/callvariants/**
33 changes: 0 additions & 33 deletions tests/modules/nf-core/universc/main.nf
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17 changes: 0 additions & 17 deletions tests/modules/nf-core/universc/nextflow.config
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68 changes: 0 additions & 68 deletions tests/modules/nf-core/universc/test.yml
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