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add test_data_base to tests
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@kubranarci
kubranarci committed Feb 4, 2025
1 parent d426f5d commit f9ae067
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Showing 6 changed files with 189 additions and 1 deletion.
4 changes: 4 additions & 0 deletions tests/germline_small.nf.test
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Expand Up @@ -12,6 +12,8 @@ nextflow_pipeline {
when {
params {
outdir = "$outputDir"
test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/variantbenchmarking'

}
}

Expand Down Expand Up @@ -42,6 +44,8 @@ nextflow_pipeline {
when {
params {
outdir = "$outputDir"
test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/variantbenchmarking'

}
}

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2 changes: 2 additions & 0 deletions tests/liftover_test.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,8 @@ nextflow_pipeline {
when {
params {
outdir = "$outputDir"
test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/variantbenchmarking'

}
}

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2 changes: 2 additions & 0 deletions tests/liftover_truth.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,8 @@ nextflow_pipeline {
when {
params {
outdir = "$outputDir"
test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/variantbenchmarking'

}
}

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2 changes: 2 additions & 0 deletions tests/somatic_indel.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,8 @@ nextflow_pipeline {
when {
params {
outdir = "$outputDir"
test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/variantbenchmarking'

}
}

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20 changes: 19 additions & 1 deletion tests/somatic_snv.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -12,12 +12,28 @@ nextflow_pipeline {
when {
params {
outdir = "$outputDir"
test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/variantbenchmarking'

}
}

then {
// stable_name: All files + folders in ${params.outdir}/ with a stable name
def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
// stable_path: All files in ${params.outdir}/ with stable content
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
assertAll(
{ assert workflow.success }
{ assert workflow.success },
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
stable_path
).match() }
)
}
}
Expand All @@ -28,6 +44,8 @@ nextflow_pipeline {
when {
params {
outdir = "$outputDir"
test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/variantbenchmarking'

}
}

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160 changes: 160 additions & 0 deletions tests/somatic_snv.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -96,5 +96,165 @@
"nextflow": "24.10.4"
},
"timestamp": "2025-01-29T17:10:57.898182832"
},
"Params: --analysis 'somatic' --variant_type 'snv' --method 'sompy'": {
"content": [
29,
null,
[
"pipeline_info",
"pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml",
"snv",
"snv/SEQC2",
"snv/SEQC2/preprocess",
"snv/SEQC2/preprocess/SEQC2.vcf.gz",
"snv/SEQC2/preprocess/SEQC2.vcf.gz.tbi",
"snv/SEQC2/stats",
"snv/SEQC2/stats/bcftools",
"snv/SEQC2/stats/bcftools/SEQC2.bcftools_stats.txt",
"snv/multiqc",
"snv/multiqc/multiqc_data",
"snv/multiqc/multiqc_data/bcftools-stats-subtypes.txt",
"snv/multiqc/multiqc_data/bcftools_stats_indel-lengths.txt",
"snv/multiqc/multiqc_data/bcftools_stats_variant_depths.txt",
"snv/multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt",
"snv/multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt",
"snv/multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt",
"snv/multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt",
"snv/multiqc/multiqc_data/multiqc.log",
"snv/multiqc/multiqc_data/multiqc_bcftools_stats.txt",
"snv/multiqc/multiqc_data/multiqc_citations.txt",
"snv/multiqc/multiqc_data/multiqc_data.json",
"snv/multiqc/multiqc_data/multiqc_general_stats.txt",
"snv/multiqc/multiqc_data/multiqc_software_versions.txt",
"snv/multiqc/multiqc_data/multiqc_sources.txt",
"snv/multiqc/multiqc_plots",
"snv/multiqc/multiqc_plots/pdf",
"snv/multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf",
"snv/multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf",
"snv/multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths.pdf",
"snv/multiqc/multiqc_plots/pdf/bcftools_stats_variant_depths.pdf",
"snv/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf",
"snv/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf",
"snv/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf",
"snv/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf",
"snv/multiqc/multiqc_plots/pdf/general_stats_table.pdf",
"snv/multiqc/multiqc_plots/png",
"snv/multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png",
"snv/multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png",
"snv/multiqc/multiqc_plots/png/bcftools_stats_indel-lengths.png",
"snv/multiqc/multiqc_plots/png/bcftools_stats_variant_depths.png",
"snv/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png",
"snv/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png",
"snv/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png",
"snv/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png",
"snv/multiqc/multiqc_plots/png/general_stats_table.png",
"snv/multiqc/multiqc_plots/svg",
"snv/multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg",
"snv/multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg",
"snv/multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths.svg",
"snv/multiqc/multiqc_plots/svg/bcftools_stats_variant_depths.svg",
"snv/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg",
"snv/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg",
"snv/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg",
"snv/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg",
"snv/multiqc/multiqc_plots/svg/general_stats_table.svg",
"snv/multiqc/multiqc_report.html",
"snv/summary",
"snv/summary/datavzrd",
"snv/summary/datavzrd/sompy",
"snv/summary/datavzrd/sompy/index.html",
"snv/summary/datavzrd/sompy/static",
"snv/summary/datavzrd/sompy/static/bootstrap-select.min.css",
"snv/summary/datavzrd/sompy/static/bootstrap-table-fixed-columns.min.css",
"snv/summary/datavzrd/sompy/static/bootstrap-table.min.css",
"snv/summary/datavzrd/sompy/static/bootstrap.min.css",
"snv/summary/datavzrd/sompy/static/bundle.js",
"snv/summary/datavzrd/sompy/static/datavzrd.css",
"snv/summary/datavzrd/sompy/test",
"snv/summary/datavzrd/sompy/test/config.js",
"snv/summary/datavzrd/sompy/test/data",
"snv/summary/datavzrd/sompy/test/data/data_1.js",
"snv/summary/datavzrd/sompy/test/functions.js",
"snv/summary/datavzrd/sompy/test/heatmap.js",
"snv/summary/datavzrd/sompy/test/index_1.html",
"snv/summary/datavzrd/sompy/test/plots",
"snv/summary/datavzrd/sompy/test/plots/plot_0.js",
"snv/summary/datavzrd/sompy/test/plots/plot_1.js",
"snv/summary/datavzrd/sompy/test/plots/plot_10.js",
"snv/summary/datavzrd/sompy/test/plots/plot_11.js",
"snv/summary/datavzrd/sompy/test/plots/plot_12.js",
"snv/summary/datavzrd/sompy/test/plots/plot_13.js",
"snv/summary/datavzrd/sompy/test/plots/plot_14.js",
"snv/summary/datavzrd/sompy/test/plots/plot_15.js",
"snv/summary/datavzrd/sompy/test/plots/plot_16.js",
"snv/summary/datavzrd/sompy/test/plots/plot_17.js",
"snv/summary/datavzrd/sompy/test/plots/plot_18.js",
"snv/summary/datavzrd/sompy/test/plots/plot_2.js",
"snv/summary/datavzrd/sompy/test/plots/plot_3.js",
"snv/summary/datavzrd/sompy/test/plots/plot_4.js",
"snv/summary/datavzrd/sompy/test/plots/plot_5.js",
"snv/summary/datavzrd/sompy/test/plots/plot_6.js",
"snv/summary/datavzrd/sompy/test/plots/plot_7.js",
"snv/summary/datavzrd/sompy/test/plots/plot_8.js",
"snv/summary/datavzrd/sompy/test/plots/plot_9.js",
"snv/summary/datavzrd/versions.yml",
"snv/summary/plots",
"snv/summary/plots/sompy",
"snv/summary/plots/sompy/metric_by_tool_sompy_mqc.png",
"snv/summary/plots/sompy/variants_by_tool_sompy_mqc.png",
"snv/summary/tables",
"snv/summary/tables/sompy",
"snv/summary/tables/sompy/sompy.regions.csv",
"snv/summary/tables/sompy/sompy.summary.csv",
"snv/test1",
"snv/test1/benchmarks",
"snv/test1/benchmarks/sompy",
"snv/test1/benchmarks/sompy/test1.SEQC2.freebayes.features.csv",
"snv/test1/benchmarks/sompy/test1.SEQC2.freebayes.metrics.json",
"snv/test1/benchmarks/sompy/test1.SEQC2.freebayes.stats.csv",
"snv/test1/preprocess",
"snv/test1/preprocess/test1.vcf.gz",
"snv/test1/preprocess/test1.vcf.gz.tbi",
"snv/test1/stats",
"snv/test1/stats/bcftools",
"snv/test1/stats/bcftools/test1.freebayes.bcftools_stats.txt",
"snv/test2",
"snv/test2/benchmarks",
"snv/test2/benchmarks/sompy",
"snv/test2/benchmarks/sompy/test2.SEQC2.manta.features.csv",
"snv/test2/benchmarks/sompy/test2.SEQC2.manta.metrics.json",
"snv/test2/benchmarks/sompy/test2.SEQC2.manta.stats.csv",
"snv/test2/preprocess",
"snv/test2/preprocess/test2.vcf.gz",
"snv/test2/preprocess/test2.vcf.gz.tbi",
"snv/test2/stats",
"snv/test2/stats/bcftools",
"snv/test2/stats/bcftools/test2.manta.bcftools_stats.txt",
"snv/test3",
"snv/test3/benchmarks",
"snv/test3/benchmarks/sompy",
"snv/test3/benchmarks/sompy/test3.SEQC2.strelka.features.csv",
"snv/test3/benchmarks/sompy/test3.SEQC2.strelka.metrics.json",
"snv/test3/benchmarks/sompy/test3.SEQC2.strelka.stats.csv",
"snv/test3/preprocess",
"snv/test3/preprocess/test3.vcf.gz",
"snv/test3/preprocess/test3.vcf.gz.tbi",
"snv/test3/stats",
"snv/test3/stats/bcftools",
"snv/test3/stats/bcftools/test3.strelka.bcftools_stats.txt"
],
[
"SEQC2.bcftools_stats.txt:md5,2a23dd61a56e7e6435a8ba4617fd793d",
"test1.freebayes.bcftools_stats.txt:md5,ca4f9a72e5cb852b78dbdf92142a4a6f",
"test2.manta.bcftools_stats.txt:md5,0806ab1c22d599b40abc4d22a129a1e2",
"test3.strelka.bcftools_stats.txt:md5,9fc6a285b83b2c2652080562ba9e94d6"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-02-04T13:25:45.366644429"
}
}

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