Skip to content

Refactor tests #163

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Aratz merged 14 commits into from
Nov 21, 2025
Merged

Refactor tests #163

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
14 commits
Select commit Hold shift + click to select a range
e249e67
Merge all mpx tests
Aratz Nov 4, 2025
73693f2
Merge all pna tests
Aratz Nov 4, 2025
aa4eedd
Execute ES in test mode for tests
Aratz Nov 5, 2025
dba750b
Add tests for pna layout
Aratz Nov 5, 2025
3948e6f
Fix pipeline test names
Aratz Nov 5, 2025
27910d8
Add stub tests for pna modules
Aratz Nov 6, 2025
5c1767f
Snapshot only file list for all nf-tests, except versions
Aratz Nov 7, 2025
61874b2
Add script to run all tests in parallel
Aratz Nov 7, 2025
9ae1187
Mark pna pipeline test as smoke test
Aratz Nov 7, 2025
ce950bf
Update CHANGELOG
Aratz Nov 7, 2025
d7770ca
Add missing ES test snapshot
Aratz Nov 7, 2025
d9304b4
Update test script
Aratz Nov 7, 2025
f3c463a
Improve output for test script
Aratz Nov 10, 2025
2e0388c
Make test script executable
Aratz Nov 10, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 4 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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

- Improve test suite by @Aratz [#163](https://github.com/nf-core/pixelator/pull/163)

## [[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
Expand Down
5 changes: 3 additions & 2 deletions modules/local/experiment_summary/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
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

Expand Down
37 changes: 22 additions & 15 deletions modules/local/experiment_summary/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,16 @@ nextflow_process {
tag "pixelator/pna"
tag "pixelator/experiment_summary"

test("PNA experiment summary - small") {


test("PNA experiment summary - stub") {

options "-stub"

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 @@ -80,18 +85,19 @@ nextflow_process {
assert path(get(0).get(1)).exists()
}
},
{ assert snapshot(process.out.versions).match("versions") },
{ assert snapshot(process.out.versions).match() },
)
}
}



test("PNA experiment summary - stub") {
test("PNA experiment summary - small") {
when {
params {
outdir = "$outputDir"
}
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 @@ -151,15 +157,16 @@ nextflow_process {
}

then {
def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
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") },
{ assert workflow.success },
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// All stable path name, with a relative path
stable_name,
process.out.versions,
).match() }
)
}
}
Expand Down
21 changes: 13 additions & 8 deletions modules/local/experiment_summary/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,26 +1,31 @@
{
"versions": {
"PNA experiment summary - small": {
"content": [
1,
[
"pixelator",
"pixelator/experiment-summary.html"
],
[
"versions.yml:md5,1c35ddcd59548b42fc730937c4263809"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-08-27T07:10:33.460197901"
"timestamp": "2025-11-07T15:10:18.392267622"
},
"stub-versions": {
"PNA experiment summary - stub": {
"content": [
[
"versions.yml:md5,1c35ddcd59548b42fc730937c4263809"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-08-27T07:13:26.253720282"
"timestamp": "2025-11-07T15:09:02.619765414"
}
}
23 changes: 10 additions & 13 deletions modules/local/pixelator/single-cell-mpx/amplicon/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },

{ assert snapshot(process.out).match() }
)
}
}
Expand All @@ -43,6 +42,7 @@ nextflow_process {
when {
params {
save_all = true
outdir = "$outputDir"
}
process {
"""
Expand All @@ -58,19 +58,16 @@ nextflow_process {
}

then {
def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
assertAll(
{ assert process.success },
{ assert workflow.success },
{ assert snapshot(
process.out.merged,
process.out.report_json,
process.out.metadata
).match()
},
{
with (process.out.log) {
assert path(get(0).get(1)).readLines().last().contains("Finished pixelator amplicon")
}
},
// Number of successful tasks
workflow.trace.succeeded().size(),
// All stable path name, with a relative path
stable_name,
process.out.versions,
).match() }
)
}
}
Expand Down
45 changes: 13 additions & 32 deletions modules/local/pixelator/single-cell-mpx/amplicon/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,45 +1,26 @@
{
"Test MPX amplicon - SCSP v1 | Immunology-I": {
"content": [
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.merged.fastq.gz:md5,b66b4946d695f8e2202e2018dcfd6a15"
]
],
[
[
{
"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:md5,5c15027e9dd0e441f8695a166817c9a5"
]
"pixelator",
"pixelator/amplicon",
"pixelator/amplicon/sample01_1k_pbmcs_scsp_v1_immunology1.merged.fastq.gz",
"pixelator/amplicon/sample01_1k_pbmcs_scsp_v1_immunology1.meta.json",
"pixelator/amplicon/sample01_1k_pbmcs_scsp_v1_immunology1.report.json",
"pixelator/logs",
"pixelator/logs/sample01_1k_pbmcs_scsp_v1_immunology1",
"pixelator/logs/sample01_1k_pbmcs_scsp_v1_immunology1/sample01_1k_pbmcs_scsp_v1_immunology1.pixelator-amplicon.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.meta.json:md5,40db76b696434ea585851070cabe8baa"
]
"versions.yml:md5,60a7a0bbc070d248db9f89ab0972c46e"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.2"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-07-28T11:06:59.496585652"
"timestamp": "2025-11-07T08:29:01.551421256"
},
"Test MPX amplicon - stub": {
"content": [
Expand Down
22 changes: 11 additions & 11 deletions modules/local/pixelator/single-cell-mpx/analysis/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,8 @@ nextflow_process {
test("Test MPX analysis - SCSP v1 | Immunology-I") {
when {
params {
save_all
save_all = true
outdir = "$outputDir"
}
process {
"""
Expand All @@ -48,17 +49,16 @@ nextflow_process {
}

then {
def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
assertAll(
{ assert process.success },
{assert path(process.out.report_json.get(0).get(1)).exists()},
{assert path(process.out.metadata.get(0).get(1)).exists()},
{assert path(process.out.dataset.get(0).get(1)).exists()},
{assert process.out.dataset.get(0).get(1).endsWith(".pxl")},
{
with (process.out.log) {
assert path(get(0).get(1)).readLines().last().contains("Finished pixelator analysis")
}
},
{ assert workflow.success },
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// All stable path name, with a relative path
stable_name,
process.out.versions,
).match() }
)
}
}
Expand Down
23 changes: 23 additions & 0 deletions modules/local/pixelator/single-cell-mpx/analysis/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,27 @@
{
"Test MPX analysis - SCSP v1 | Immunology-I": {
"content": [
1,
[
"pixelator",
"pixelator/analysis",
"pixelator/analysis/sample01_1k_pbmcs_scsp_v1_immunology1.analysis.dataset.pxl",
"pixelator/analysis/sample01_1k_pbmcs_scsp_v1_immunology1.meta.json",
"pixelator/analysis/sample01_1k_pbmcs_scsp_v1_immunology1.report.json",
"pixelator/logs",
"pixelator/logs/sample01_1k_pbmcs_scsp_v1_immunology1",
"pixelator/logs/sample01_1k_pbmcs_scsp_v1_immunology1/sample01_1k_pbmcs_scsp_v1_immunology1.pixelator-analysis.log"
],
[
"versions.yml:md5,294239a503f1320c924038c6554443a2"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-11-07T10:12:24.48353731"
},
"Test MPX analysis - stub": {
"content": [
{
Expand Down
27 changes: 10 additions & 17 deletions modules/local/pixelator/single-cell-mpx/annotate/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@ nextflow_process {
when {
params {
save_all = true
outdir = "$outputDir"
}
process {
"""
Expand All @@ -55,24 +56,16 @@ nextflow_process {
}

then {
def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
assertAll(
{ assert process.success },
{assert path(process.out.report_json.get(0).get(1)).exists()},
{assert path(process.out.metadata.get(0).get(1)).exists()},
{
with (process.out.dataset.get(0)) {
assert path(get(1)).zip.extract("adata.h5ad").exists()
assert path(get(1)).zip.extract("edgelist.parquet").exists()
assert snapshot(
path(get(1)).zip.extract("metadata.json")
).match("pxl")
}
},
{
with (process.out.log) {
assert path(get(0).get(1)).readLines().last().contains("Finished pixelator annotate")
}
},
{ assert workflow.success },
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// All stable path name, with a relative path
stable_name,
process.out.versions,
).match() }
)
}
}
Expand Down
19 changes: 16 additions & 3 deletions modules/local/pixelator/single-cell-mpx/annotate/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,13 +1,26 @@
{
"pxl": {
"Test MPX annotate - SCSP v1 | Immunology-I": {
"content": [
"metadata.json:md5,82b35492f5e5067481c04c8612f466ee"
1,
[
"pixelator",
"pixelator/annotate",
"pixelator/annotate/sample01_1k_pbmcs_scsp_v1_immunology1.annotate.dataset.pxl",
"pixelator/annotate/sample01_1k_pbmcs_scsp_v1_immunology1.meta.json",
"pixelator/annotate/sample01_1k_pbmcs_scsp_v1_immunology1.report.json",
"pixelator/logs",
"pixelator/logs/sample01_1k_pbmcs_scsp_v1_immunology1",
"pixelator/logs/sample01_1k_pbmcs_scsp_v1_immunology1/sample01_1k_pbmcs_scsp_v1_immunology1.pixelator-annotate.log"
],
[
"versions.yml:md5,f96c065a146a6d0667467f30beb8092b"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-10-31T13:30:45.331289297"
"timestamp": "2025-11-07T10:13:35.389069003"
},
"Test MPX annotate - stub": {
"content": [
Expand Down
Loading