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Refactor nf-tests #161

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2c798a5
Merge all mpx tests
Aratz Nov 4, 2025
9b03d63
Merge all pna tests
Aratz Nov 4, 2025
fb38632
Remove pipeline stub tests
Aratz Nov 4, 2025
501c3d2
Remove all module stub tests
Aratz Nov 4, 2025
6f51730
Remove demux multiple chunk test
Aratz Nov 4, 2025
7874ff7
Remove pna subworkflow tests
Aratz Nov 4, 2025
d8b4a0a
Remove subworkflow stub
Aratz Nov 4, 2025
7ec18bc
Execute ES in test mode for tests
Aratz Nov 5, 2025
1038d8f
Add tests for pna layout
Aratz Nov 5, 2025
866c383
Recompute snapshots
Aratz Nov 5, 2025
b9c444f
Merge remote-tracking branch 'origin/dev' into fix/refactor_tests
Aratz Nov 5, 2025
a6004b8
Update CHANGELOG
Aratz Nov 5, 2025
8cfdddc
Fix pipeline test names
Aratz Nov 5, 2025
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## dev - xxxx-xx-xx

### Enhancements & fixes

- Refactor nf-tests by @Aratz [#161](https://github.com/nf-core/pixelator/pull/161)

## [[2.2.0](https://github.com/nf-core/pixelator/releases/tag/2.2.0)] - 2025-11-02

This new minor version of nf-core/pixelator introduces new panel files with clearer names. These new
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5 changes: 3 additions & 2 deletions modules/local/experiment_summary/main.nf
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Expand Up @@ -24,13 +24,14 @@ process EXPERIMENT_SUMMARY {
path("versions.yml") , emit: versions

script:

def args = task.ext.args ?: ''
"""
# Copy the full quarto dir from the read-only image into the workdir
cp -r /workspace/inst/quarto/ ./quarto/
quarto render ./quarto/pixelatorES.qmd \\
-P sample_sheet="\$PWD/${samplesheet_path}" \\
-P data_folder="\$PWD/results/"
-P data_folder="\$PWD/results/" \\
$args \\

mv ./quarto/pixelatorES.html experiment-summary.html

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81 changes: 1 addition & 80 deletions modules/local/experiment_summary/tests/main.nf.test
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Expand Up @@ -12,7 +12,7 @@ nextflow_process {
when {
process {
"""
input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_pna_es.csv', checkIfExists: true) ]
input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_pna.csv', checkIfExists: true) ]
input[1] = [
[id:'all', design:'pna-2', panel:'proxiome-immuno-155', technology:'pna' ],
// amplicon
Expand Down Expand Up @@ -84,83 +84,4 @@ nextflow_process {
)
}
}



test("PNA experiment summary - stub") {
when {
process {
"""
input[0] = [ file(params.pipelines_testdata_base_path + 'samplesheet/pna/samplesheet_pna_es.csv', checkIfExists: true) ]
input[1] = [
[id:'all', design:'pna-2', panel:'proxiome-immuno-155', technology:'pna' ],
// amplicon
[
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/amplicon/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true),
],
// demux
[
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/demux/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true),
],
// (combined collapse)
[
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/collapse/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true),
],
// graph
[
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/graph/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true),
],
// denoise
[
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/denoise/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true),
],
// analysis
[
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/analysis/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true),
],
// layout
[
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.layout.pxl', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_filtered_S7.report.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_unfiltered_S7.layout.pxl', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_unfiltered_S7.meta.json', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/pna/modules/layout/PNA055_Sample07_unfiltered_S7.report.json', checkIfExists: true),
]
]
"""
}
}

then {
assertAll(
{ assert process.success },
{
with(process.out.html) {
assert path(get(0).get(1)).endsWith("experiment-summary.html")
assert path(get(0).get(1)).exists()
}
},
{ assert snapshot(process.out.versions).match("stub-versions") },
)
}
}
}
12 changes: 0 additions & 12 deletions modules/local/experiment_summary/tests/main.nf.test.snap
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Expand Up @@ -10,17 +10,5 @@
"nextflow": "25.04.6"
},
"timestamp": "2025-08-27T07:10:33.460197901"
},
"stub-versions": {
"content": [
[
"versions.yml:md5,1c35ddcd59548b42fc730937c4263809"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-08-27T07:13:26.253720282"
}
}
30 changes: 0 additions & 30 deletions modules/local/pixelator/single-cell-mpx/amplicon/tests/main.nf.test
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Expand Up @@ -9,36 +9,6 @@ nextflow_process {
tag "pixelator/single_cell_mpx_amplicon"


test("Test MPX amplicon - stub") {

options "-stub"

when {
params {
save_all = true
}
process {
"""
input[0] = [
[ id:'sample01_1k_pbmcs_scsp_v1_immunology1', design:'D21', panel:'human-sc-immunology-spatial-proteomics-1', technology:'mpx' ],
[
file(params.pipelines_testdata_base_path + 'testdata/mpx/fastq/v1/sample01_1k_pbmcs_scsp_v1_immunology1_R1.fastq.gz', checkIfExists: true),
file(params.pipelines_testdata_base_path + 'testdata/mpx/fastq/v1/sample01_1k_pbmcs_scsp_v1_immunology1_R2.fastq.gz', checkIfExists: true)
]
]
"""
}
}

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

)
}
}

test("Test MPX amplicon - SCSP v1 | Immunology-I") {
when {
params {
Expand Down
105 changes: 0 additions & 105 deletions modules/local/pixelator/single-cell-mpx/amplicon/tests/main.nf.test.snap
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Expand Up @@ -40,110 +40,5 @@
"nextflow": "25.04.2"
},
"timestamp": "2025-07-28T11:06:59.496585652"
},
"Test MPX amplicon - stub": {
"content": [
{
"0": [
[
{
"id": "sample01_1k_pbmcs_scsp_v1_immunology1",
"design": "D21",
"panel": "human-sc-immunology-spatial-proteomics-1",
"technology": "mpx"
},
"sample01_1k_pbmcs_scsp_v1_immunology1.merged.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [
[
{
"id": "sample01_1k_pbmcs_scsp_v1_immunology1",
"design": "D21",
"panel": "human-sc-immunology-spatial-proteomics-1",
"technology": "mpx"
},
"sample01_1k_pbmcs_scsp_v1_immunology1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
[
{
"id": "sample01_1k_pbmcs_scsp_v1_immunology1",
"design": "D21",
"panel": "human-sc-immunology-spatial-proteomics-1",
"technology": "mpx"
},
"sample01_1k_pbmcs_scsp_v1_immunology1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [
[
{
"id": "sample01_1k_pbmcs_scsp_v1_immunology1",
"design": "D21",
"panel": "human-sc-immunology-spatial-proteomics-1",
"technology": "mpx"
},
"sample01_1k_pbmcs_scsp_v1_immunology1.pixelator-amplicon.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"4": [
"versions.yml:md5,60a7a0bbc070d248db9f89ab0972c46e"
],
"log": [
[
{
"id": "sample01_1k_pbmcs_scsp_v1_immunology1",
"design": "D21",
"panel": "human-sc-immunology-spatial-proteomics-1",
"technology": "mpx"
},
"sample01_1k_pbmcs_scsp_v1_immunology1.pixelator-amplicon.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"merged": [
[
{
"id": "sample01_1k_pbmcs_scsp_v1_immunology1",
"design": "D21",
"panel": "human-sc-immunology-spatial-proteomics-1",
"technology": "mpx"
},
"sample01_1k_pbmcs_scsp_v1_immunology1.merged.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"metadata": [
[
{
"id": "sample01_1k_pbmcs_scsp_v1_immunology1",
"design": "D21",
"panel": "human-sc-immunology-spatial-proteomics-1",
"technology": "mpx"
},
"sample01_1k_pbmcs_scsp_v1_immunology1.meta.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"report_json": [
[
{
"id": "sample01_1k_pbmcs_scsp_v1_immunology1",
"design": "D21",
"panel": "human-sc-immunology-spatial-proteomics-1",
"technology": "mpx"
},
"sample01_1k_pbmcs_scsp_v1_immunology1.report.json:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,60a7a0bbc070d248db9f89ab0972c46e"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-10-31T13:29:04.145467489"
}
}
23 changes: 0 additions & 23 deletions modules/local/pixelator/single-cell-mpx/analysis/tests/main.nf.test
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Expand Up @@ -9,29 +9,6 @@ nextflow_process {
tag "pixelator/single_cell_mpx_analysis"


test("Test MPX analysis - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'sample01_1k_pbmcs_scsp_v1_immunology1', design:'D21', panel:'human-sc-immunology-spatial-proteomics-1', technology:'mpx' ],
file(params.pipelines_testdata_base_path + 'testdata/mpx/modules/annotate/sample01_1k_pbmcs_scsp_v1_immunology1.annotate.dataset.pxl', checkIfExists: true)
]
"""
}
}

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

test("Test MPX analysis - SCSP v1 | Immunology-I") {
when {
params {
Expand Down
26 changes: 0 additions & 26 deletions modules/local/pixelator/single-cell-mpx/annotate/tests/main.nf.test
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Expand Up @@ -9,32 +9,6 @@ nextflow_process {
tag "pixelator/single_cell_mpx_annotate"


test("Test MPX annotate - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'sample01_1k_pbmcs_scsp_v1_immunology1', design:'D21', panel:'human-sc-immunology-spatial-proteomics-1', technology:'mpx' ],
file(params.pipelines_testdata_base_path + 'testdata/mpx/modules/graph/sample01_1k_pbmcs_scsp_v1_immunology1.edgelist.parquet', checkIfExists: true),
[],
"human-sc-immunology-spatial-proteomics-1"
]
"""
}
}

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

)
}
}

test("Test MPX annotate - SCSP v1 | Immunology-I") {
options "--save_all"

Expand Down
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