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Test data uses paths instead of config map #2877

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merged 7 commits into from
Jun 26, 2024
Merged

Test data uses paths instead of config map #2877

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0e9640f
Module test data uses paths rather than config map
adamrtalbot Mar 19, 2024
bb53c9d
Update subworkflow test data
adamrtalbot Mar 19, 2024
f6bd633
[automated] Update CHANGELOG.md
nf-core-bot Mar 19, 2024
065d1c3
CHANGELOG
adamrtalbot Mar 19, 2024
6bf5389
Auto changelog did it all for me
adamrtalbot Mar 19, 2024
79e445e
Merge branch 'dev' into 2858_test_data_uses_paths
adamrtalbot Mar 19, 2024
af2cf15
Merge branch 'dev' into 2858_test_data_uses_paths
adamrtalbot Jun 26, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,8 @@
- fix(collectfile): sort true for methods_description_mqc.yaml ([#2947](https://github.com/nf-core/tools/pull/2947))
- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.4.3 ([#2951](https://github.com/nf-core/tools/pull/2951))
- Restructure CHANGELOG.md ([#2954](https://github.com/nf-core/tools/pull/2954))
- fix: ensure path object converted to string before stripping quotes ([#2878](https://github.com/nf-core/tools/pull/2878))
- Test data uses paths instead of config map ([#2877](https://github.com/nf-core/tools/pull/2877))

## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]

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10 changes: 5 additions & 5 deletions nf_core/module-template/tests/main.nf.test.j2
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Expand Up @@ -28,10 +28,10 @@ nextflow_process {
{% if has_meta %}
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
]
{%- else %}
input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
{%- endif %}
"""
}
Expand Down Expand Up @@ -60,10 +60,10 @@ nextflow_process {
{% if has_meta %}
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
]
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
]
{%- else %}
input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
{%- endif %}
"""
}
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14 changes: 8 additions & 6 deletions nf_core/subworkflow-template/tests/main.nf.test.j2
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Expand Up @@ -22,12 +22,14 @@ nextflow_workflow {
workflow {
"""
// TODO nf-core: define inputs of the workflow here. Example:
input[0] = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
]
input[1] = [ [ id:'genome' ],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
]
input[1] = [
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
]
"""
}
}
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