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@maxulysse
maxulysse committed Oct 29, 2024
1 parent fa5fbbc commit fe5c75a
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75 changes: 75 additions & 0 deletions tests/annotation-snpeff.nf.test
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nextflow_pipeline {

name "Test pipeline"
script "../main.nf"
tag "pipeline"
tag "pipeline_sarek"

test("Run with profile test | --tools snpeff --download_cache") {

when {
params {
modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
outdir = "$outputDir"
input = "${projectDir}/tests/csv/3.0/vcf_single.csv"
step = 'annotate'
download_cache = true
tools = 'snpeff'
}
}

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 ${params.outdir}/ with stable content
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
assertAll(
{ assert workflow.success},
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
stable_path
).match() }
)
}
}

test("Run with profile test | --tools snpeff") {

when {
params {
modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
outdir = "$outputDir"
input = "${projectDir}/tests/csv/3.0/vcf_single.csv"
step = 'annotate'
snpeff_cache = 's3://annotation-cache/snpeff_cache/'
tools = 'snpeff'
}
}

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 ${params.outdir}/ with stable content
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
assertAll(
{ assert workflow.success},
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
stable_path
).match() }
)
}
}
}
197 changes: 197 additions & 0 deletions tests/annotation-snpeff.nf.test.snap
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{
"Run with profile test | --tools snpeff --download_cache": {
"content": [
4,
{
"SNPEFF_SNPEFF": {
"snpeff": "5.1d"
},
"TABIX_BGZIPTABIX": {
"tabix": 1.2
},
"Workflow": {
"nf-core/sarek": "v3.5.0dev"
}
},
[
"annotation",
"annotation/test",
"annotation/test/test_snpEff.ann.vcf.gz",
"annotation/test/test_snpEff.ann.vcf.gz.tbi",
"cache",
"cache/snpeff_cache",
"cache/snpeff_cache/WBcel235.105",
"cache/snpeff_cache/WBcel235.105/sequence.I.bin",
"cache/snpeff_cache/WBcel235.105/sequence.II.bin",
"cache/snpeff_cache/WBcel235.105/sequence.III.bin",
"cache/snpeff_cache/WBcel235.105/sequence.IV.bin",
"cache/snpeff_cache/WBcel235.105/sequence.V.bin",
"cache/snpeff_cache/WBcel235.105/sequence.X.bin",
"cache/snpeff_cache/WBcel235.105/sequence.bin",
"cache/snpeff_cache/WBcel235.105/snpEffectPredictor.bin",
"cache/versions.yml",
"csv",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
"multiqc/multiqc_data/multiqc_general_stats.txt",
"multiqc/multiqc_data/multiqc_snpeff.txt",
"multiqc/multiqc_data/multiqc_software_versions.txt",
"multiqc/multiqc_data/multiqc_sources.txt",
"multiqc/multiqc_data/snpeff_effects.txt",
"multiqc/multiqc_data/snpeff_qualities.txt",
"multiqc/multiqc_data/snpeff_variant_effects_region.txt",
"multiqc/multiqc_plots",
"multiqc/multiqc_plots/pdf",
"multiqc/multiqc_plots/pdf/general_stats_table.pdf",
"multiqc/multiqc_plots/pdf/snpeff_effects-cnt.pdf",
"multiqc/multiqc_plots/pdf/snpeff_effects-pct.pdf",
"multiqc/multiqc_plots/pdf/snpeff_qualities.pdf",
"multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-cnt.pdf",
"multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-log.pdf",
"multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-pct-log.pdf",
"multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-pct.pdf",
"multiqc/multiqc_plots/png",
"multiqc/multiqc_plots/png/general_stats_table.png",
"multiqc/multiqc_plots/png/snpeff_effects-cnt.png",
"multiqc/multiqc_plots/png/snpeff_effects-pct.png",
"multiqc/multiqc_plots/png/snpeff_qualities.png",
"multiqc/multiqc_plots/png/snpeff_variant_effects_region-cnt.png",
"multiqc/multiqc_plots/png/snpeff_variant_effects_region-log.png",
"multiqc/multiqc_plots/png/snpeff_variant_effects_region-pct-log.png",
"multiqc/multiqc_plots/png/snpeff_variant_effects_region-pct.png",
"multiqc/multiqc_plots/svg",
"multiqc/multiqc_plots/svg/general_stats_table.svg",
"multiqc/multiqc_plots/svg/snpeff_effects-cnt.svg",
"multiqc/multiqc_plots/svg/snpeff_effects-pct.svg",
"multiqc/multiqc_plots/svg/snpeff_qualities.svg",
"multiqc/multiqc_plots/svg/snpeff_variant_effects_region-cnt.svg",
"multiqc/multiqc_plots/svg/snpeff_variant_effects_region-log.svg",
"multiqc/multiqc_plots/svg/snpeff_variant_effects_region-pct-log.svg",
"multiqc/multiqc_plots/svg/snpeff_variant_effects_region-pct.svg",
"multiqc/multiqc_report.html",
"pipeline_info",
"pipeline_info/nf_core_sarek_software_mqc_versions.yml",
"reports",
"reports/snpeff",
"reports/snpeff/test",
"reports/snpeff/test/snpEff_summary.html",
"reports/snpeff/test/test_snpEff.csv",
"reports/snpeff/test/test_snpEff.genes.txt"
],
[
"sequence.I.bin:md5,2fd1694bd91cf7952cbad8cfed161e53",
"sequence.II.bin:md5,bacedbdea89508e108223767fa260a4c",
"sequence.III.bin:md5,444118a9fb9d0a03c37e86094d8e52a9",
"sequence.IV.bin:md5,ff756628faa0b71cd65495668c3d82b5",
"sequence.V.bin:md5,d6ad5476162ac45829f719dd4ee3f4e7",
"sequence.X.bin:md5,b79bec6cc8f96b8373dac56bab5d0a6c",
"sequence.bin:md5,ec2bc2ae81755ab90fcf1848bc7ce41f",
"snpEffectPredictor.bin:md5,1d99251d0405f0a42913ed8b5b2c2fa7",
"versions.yml:md5,e9698b9ccf3bb151631d1e07fbae8397",
"multiqc_citations.txt:md5,47e39f5f5f05da6bc38d13aa81fe8b6e",
"multiqc_snpeff.txt:md5,03a2b1c461cb6e5cccac64033a2f6526",
"snpeff_effects.txt:md5,3c5e9a1c191b77c781dc4d033b1dd1f7",
"snpeff_qualities.txt:md5,4c059b4e8bf0a64940ad1d6e30efd3a6",
"snpeff_variant_effects_region.txt:md5,05efd324edadced17ba3cd2b7714af57",
"snpEff_summary.html:md5,b0658aa728db5acfb5fae433d411f06a",
"test_snpEff.csv:md5,d6ca9f83555aa18445d565692b5ee8c2",
"test_snpEff.genes.txt:md5,130536bf0237d7f3f746d32aaa32840a"
]
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-10-29T09:02:01.062023"
},
"Run with profile test | --tools snpeff": {
"content": [
3,
{
"SNPEFF_SNPEFF": {
"snpeff": "5.1d"
},
"TABIX_BGZIPTABIX": {
"tabix": 1.2
},
"Workflow": {
"nf-core/sarek": "v3.5.0dev"
}
},
[
"annotation",
"annotation/test",
"annotation/test/test_snpEff.ann.vcf.gz",
"annotation/test/test_snpEff.ann.vcf.gz.tbi",
"csv",
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
"multiqc/multiqc_data/multiqc_general_stats.txt",
"multiqc/multiqc_data/multiqc_snpeff.txt",
"multiqc/multiqc_data/multiqc_software_versions.txt",
"multiqc/multiqc_data/multiqc_sources.txt",
"multiqc/multiqc_data/snpeff_effects.txt",
"multiqc/multiqc_data/snpeff_qualities.txt",
"multiqc/multiqc_data/snpeff_variant_effects_region.txt",
"multiqc/multiqc_plots",
"multiqc/multiqc_plots/pdf",
"multiqc/multiqc_plots/pdf/general_stats_table.pdf",
"multiqc/multiqc_plots/pdf/snpeff_effects-cnt.pdf",
"multiqc/multiqc_plots/pdf/snpeff_effects-pct.pdf",
"multiqc/multiqc_plots/pdf/snpeff_qualities.pdf",
"multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-cnt.pdf",
"multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-log.pdf",
"multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-pct-log.pdf",
"multiqc/multiqc_plots/pdf/snpeff_variant_effects_region-pct.pdf",
"multiqc/multiqc_plots/png",
"multiqc/multiqc_plots/png/general_stats_table.png",
"multiqc/multiqc_plots/png/snpeff_effects-cnt.png",
"multiqc/multiqc_plots/png/snpeff_effects-pct.png",
"multiqc/multiqc_plots/png/snpeff_qualities.png",
"multiqc/multiqc_plots/png/snpeff_variant_effects_region-cnt.png",
"multiqc/multiqc_plots/png/snpeff_variant_effects_region-log.png",
"multiqc/multiqc_plots/png/snpeff_variant_effects_region-pct-log.png",
"multiqc/multiqc_plots/png/snpeff_variant_effects_region-pct.png",
"multiqc/multiqc_plots/svg",
"multiqc/multiqc_plots/svg/general_stats_table.svg",
"multiqc/multiqc_plots/svg/snpeff_effects-cnt.svg",
"multiqc/multiqc_plots/svg/snpeff_effects-pct.svg",
"multiqc/multiqc_plots/svg/snpeff_qualities.svg",
"multiqc/multiqc_plots/svg/snpeff_variant_effects_region-cnt.svg",
"multiqc/multiqc_plots/svg/snpeff_variant_effects_region-log.svg",
"multiqc/multiqc_plots/svg/snpeff_variant_effects_region-pct-log.svg",
"multiqc/multiqc_plots/svg/snpeff_variant_effects_region-pct.svg",
"multiqc/multiqc_report.html",
"pipeline_info",
"pipeline_info/nf_core_sarek_software_mqc_versions.yml",
"reports",
"reports/snpeff",
"reports/snpeff/test",
"reports/snpeff/test/snpEff_summary.html",
"reports/snpeff/test/test_snpEff.csv",
"reports/snpeff/test/test_snpEff.genes.txt"
],
[
"multiqc_citations.txt:md5,47e39f5f5f05da6bc38d13aa81fe8b6e",
"multiqc_snpeff.txt:md5,03a2b1c461cb6e5cccac64033a2f6526",
"snpeff_effects.txt:md5,3c5e9a1c191b77c781dc4d033b1dd1f7",
"snpeff_qualities.txt:md5,4c059b4e8bf0a64940ad1d6e30efd3a6",
"snpeff_variant_effects_region.txt:md5,05efd324edadced17ba3cd2b7714af57",
"snpEff_summary.html:md5,990f2f24d5f37d177bca479706135be7",
"test_snpEff.csv:md5,f077b95576c7d137a2fd1d096aa5434c",
"test_snpEff.genes.txt:md5,130536bf0237d7f3f746d32aaa32840a"
]
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-10-29T09:04:02.127501"
}
}
9 changes: 0 additions & 9 deletions tests/config/pytesttags.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -461,15 +461,6 @@ merge:
- tests/csv/3.0/vcf_single.csv
- tests/test_annotation_merge.yml

## snpeff
snpeff:
- conf/modules/annotate.config
- modules/nf-core/snpeff/snpeff/**
- modules/nf-core/tabix/bgziptabix/**
- subworkflows/nf-core/vcf_annotate_snpeff/**
- tests/csv/3.0/vcf_single.csv
- tests/test_annotation_snpeff.yml

## bcfann
bcfann:
- conf/modules/annotate.config
Expand Down
27 changes: 0 additions & 27 deletions tests/test_annotation_snpeff.yml
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