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update test assertions in modules template to current recommendations and remove single_end from example meta value #3815

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Merged
mashehu merged 7 commits into from
Oct 10, 2025
Merged

update test assertions in modules template to current recommendations and remove single_end from example meta value #3815

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26f9884
update modules test assertions
mashehu Oct 7, 2025
12a4d47
[automated] Update CHANGELOG.md
nf-core-bot Oct 7, 2025
5fe18d9
update also subworkflow test template
mashehu Oct 7, 2025
ea8781d
remove `single_end` from modules test template
mashehu Oct 7, 2025
e499e94
Merge branch 'add-example-capture-to-modules-test' of github.com:mash…
mashehu Oct 7, 2025
a7749bb
[automated] Update CHANGELOG.md
nf-core-bot Oct 7, 2025
435164d
apply code suggestions
mashehu Oct 8, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@
- Support modules with `exec:` blocks ([#3633](https://github.com/nf-core/tools/pull/3633))
- feat: nf-core modules bump-version supports specifying the toolkit ([#3608](https://github.com/nf-core/tools/pull/3608))
- Override example keywords in modules test ([#3801](https://github.com/nf-core/tools/pull/3801))
- update test assertions in modules template to current recommendations and remove `single_end` from example meta value ([#3815](https://github.com/nf-core/tools/pull/3815))

### Subworkflows

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19 changes: 12 additions & 7 deletions nf_core/module-template/tests/main.nf.test.j2
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Expand Up @@ -27,7 +27,7 @@ nextflow_process {
// TODO nf-core: define inputs of the process here. Example:
{% if has_meta %}
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
]
{%- else %}
Expand All @@ -38,9 +38,12 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
//TODO nf-core: Add all required assertions to verify the test output.
// See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
)
Expand All @@ -59,7 +62,7 @@ nextflow_process {
// TODO nf-core: define inputs of the process here. Example:
{% if has_meta %}
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
]
{%- else %}
Expand All @@ -70,10 +73,12 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
//TODO nf-core: Add all required assertions to verify the test output.
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
)
}

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9 changes: 5 additions & 4 deletions nf_core/subworkflow-template/tests/main.nf.test.j2
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Expand Up @@ -33,12 +33,13 @@ nextflow_workflow {
"""
}
}

then {
assert workflow.success
assertAll(
{ assert workflow.success},
{ assert snapshot(workflow.out).match()}
//TODO nf-core: Add all required assertions to verify the test output.
{ assert snapshot(
workflow.out
//TODO nf-core: Add all required assertions to verify the test output.
).match() }
)
}
}
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