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Merge pull request #1661 from maxulysse/pipeline_test
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add pipeline level tests
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@maxulysse
maxulysse authored Oct 1, 2024
2 parents 4c664f4 + c1ab3de commit 6e7655f
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome`
- [1657](https://github.com/nf-core/sarek/pull/1657) - Update all actions used in the GHA CI
- [1661](https://github.com/nf-core/sarek/pull/1661) - nf-test pipeline level tests

### Removed

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4 changes: 4 additions & 0 deletions nf-test.config
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Expand Up @@ -3,4 +3,8 @@ config {
workDir ".nf-test"
configFile "conf/test.config"
profile "test"

plugins {
load "nft-utils@0.0.1"
}
}
13 changes: 13 additions & 0 deletions tests/.nftignore
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csv/*.csv
multiqc/multiqc_data/gatk_base_recalibrator.txt
multiqc/multiqc_data/multiqc.log
multiqc/multiqc_data/multiqc_data.json
multiqc/multiqc_data/multiqc_general_stats.txt
multiqc/multiqc_data/multiqc_picard_dups.txt
multiqc/multiqc_data/multiqc_sources.txt
multiqc/multiqc_report.html
pipeline_info/*.{html,json,txt,yml}
preprocessing/**/*.{md,recal}.{cram,cram.crai,table}
reports/fastqc/**/*_fastqc.{html,zip}
reports/markduplicates/**/*.md.cram.metrics
variant_calling/**/*.vcf.{gz,gz.tbi}
22 changes: 16 additions & 6 deletions tests/main.nf.test
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Expand Up @@ -9,17 +9,27 @@ nextflow_pipeline {

when {
params {
outdir = "results"
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
input = "$projectDir/tests/csv/3.0/fastq_pair.csv"
outdir = "$outputDir"
}
}

then {
// stable_name: All files + folders in ${params.outdir}/ with a stable name
def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
// stable_path: All files in ${params.outdir}/ with stable content
def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
assertAll(
{ assert workflow.success }
{ assert workflow.success},
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
// All stable paths
stable_name*.name,
// All files with stable contents
stable_path
).match() }
)
}
}
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176 changes: 176 additions & 0 deletions tests/main.nf.test.snap
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{
"Run with profile test": {
"content": [
23,
{
"BCFTOOLS_STATS": {
"bcftools": 1.2
},
"BWAMEM1_MEM": {
"bwa": "0.7.18-r1243-dirty",
"samtools": 1.2
},
"FASTQC": {
"fastqc": "0.12.1"
},
"GATK4_APPLYBQSR": {
"gatk4": "4.5.0.0"
},
"GATK4_BASERECALIBRATOR": {
"gatk4": "4.5.0.0"
},
"GATK4_MARKDUPLICATES": {
"gatk4": "4.5.0.0",
"samtools": "1.19.2"
},
"INDEX_CRAM": {
"samtools": 1.2
},
"MOSDEPTH": {
"mosdepth": "0.3.8"
},
"SAMTOOLS_STATS": {
"samtools": 1.2
},
"STRELKA_SINGLE": {
"strelka": "2.9.10"
},
"VCFTOOLS_TSTV_COUNT": {
"vcftools": "0.1.16"
},
"Workflow": {
"nf-core/sarek": "v3.5.0dev"
}
},
[
"csv",
"markduplicates.csv",
"markduplicates_no_table.csv",
"recalibrated.csv",
"variantcalled.csv",
"multiqc",
"multiqc_data",
"gatk_base_recalibrator.txt",
"mosdepth_cov_dist.txt",
"mosdepth_cumcov_dist.txt",
"mosdepth_perchrom.txt",
"multiqc.log",
"multiqc_bcftools_stats.txt",
"multiqc_citations.txt",
"multiqc_data.json",
"multiqc_fastqc.txt",
"multiqc_general_stats.txt",
"multiqc_picard_dups.txt",
"multiqc_samtools_stats.txt",
"multiqc_software_versions.txt",
"multiqc_sources.txt",
"picard_histogram.txt",
"picard_histogram_1.txt",
"picard_histogram_2.txt",
"vcftools_tstv_by_count.txt",
"vcftools_tstv_by_qual.txt",
"multiqc_plots",
"multiqc_report.html",
"pipeline_info",
"nf_core_sarek_software_mqc_versions.yml",
"preprocessing",
"markduplicates",
"test",
"test.md.cram",
"test.md.cram.crai",
"recal_table",
"test",
"test.recal.table",
"recalibrated",
"test",
"test.recal.cram",
"test.recal.cram.crai",
"reference",
"reports",
"bcftools",
"strelka",
"test",
"test.strelka.variants.bcftools_stats.txt",
"fastqc",
"test-test_L1",
"test-test_L1_1_fastqc.html",
"test-test_L1_1_fastqc.zip",
"test-test_L1_2_fastqc.html",
"test-test_L1_2_fastqc.zip",
"test-test_L2",
"test-test_L2_1_fastqc.html",
"test-test_L2_1_fastqc.zip",
"test-test_L2_2_fastqc.html",
"test-test_L2_2_fastqc.zip",
"markduplicates",
"test",
"test.md.cram.metrics",
"mosdepth",
"test",
"test.md.mosdepth.global.dist.txt",
"test.md.mosdepth.region.dist.txt",
"test.md.mosdepth.summary.txt",
"test.md.regions.bed.gz",
"test.md.regions.bed.gz.csi",
"test.recal.mosdepth.global.dist.txt",
"test.recal.mosdepth.region.dist.txt",
"test.recal.mosdepth.summary.txt",
"test.recal.regions.bed.gz",
"test.recal.regions.bed.gz.csi",
"samtools",
"test",
"test.md.cram.stats",
"test.recal.cram.stats",
"vcftools",
"strelka",
"test",
"test.strelka.variants.FILTER.summary",
"test.strelka.variants.TsTv.count",
"test.strelka.variants.TsTv.qual",
"variant_calling",
"strelka",
"test",
"test.strelka.genome.vcf.gz",
"test.strelka.genome.vcf.gz.tbi",
"test.strelka.variants.vcf.gz",
"test.strelka.variants.vcf.gz.tbi"
],
[
"mosdepth_cov_dist.txt:md5,eadafaa5473dd49daadb7b4696c6b7f9",
"mosdepth_cumcov_dist.txt:md5,8d0d7cb485a7bffb07da17b28f827120",
"mosdepth_perchrom.txt:md5,264db67a99d2c90ea7b075e33c201b77",
"multiqc_bcftools_stats.txt:md5,103ba59d44fc60e9308e64bbd0d0e504",
"multiqc_citations.txt:md5,4660dd5d8757841ed75dca3a90d21617",
"multiqc_fastqc.txt:md5,bde0d0bffa62228b33fb68b7e25b6ff8",
"multiqc_samtools_stats.txt:md5,0f1e4c6c497d9a952765f9f3068ea4b9",
"multiqc_software_versions.txt:md5,2c9d16da278a231b0dc4c4cb5c08e626",
"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"vcftools_tstv_by_count.txt:md5,327f731f65de167c7cfcbb30a5f04079",
"vcftools_tstv_by_qual.txt:md5,911bc05c5169149dbb0b068f65b4274a",
"test.strelka.variants.bcftools_stats.txt:md5,86bd4938eed920d36f3f5937102a2967",
"test.md.mosdepth.global.dist.txt:md5,b61e1acee11a6ddf7ce3232a5948a6a0",
"test.md.mosdepth.region.dist.txt:md5,1a382f98d488d2ae3df83a0d87caafc1",
"test.md.mosdepth.summary.txt:md5,839108358878ada89e1eaddf6e0541ba",
"test.md.regions.bed.gz:md5,6fdaec99e739dc0f47fe55dd64dfe93e",
"test.md.regions.bed.gz.csi:md5,5f9c60279af78e3aeafc96a8c11fb35f",
"test.recal.mosdepth.global.dist.txt:md5,b61e1acee11a6ddf7ce3232a5948a6a0",
"test.recal.mosdepth.region.dist.txt:md5,1a382f98d488d2ae3df83a0d87caafc1",
"test.recal.mosdepth.summary.txt:md5,839108358878ada89e1eaddf6e0541ba",
"test.recal.regions.bed.gz:md5,6fdaec99e739dc0f47fe55dd64dfe93e",
"test.recal.regions.bed.gz.csi:md5,5f9c60279af78e3aeafc96a8c11fb35f",
"test.md.cram.stats:md5,c4dc6487d0b8b8a74c26ea1ef4e17f6f",
"test.recal.cram.stats:md5,38bcc10d0464b259551db3b5356610ca",
"test.strelka.variants.FILTER.summary:md5,ad417bc96d31223f61170987975d8128",
"test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
"test.strelka.variants.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-10-01T10:33:51.201431"
}
}

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