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nf-test test-minimal #1145

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58922ad
Add test_minimal nf-test
TCLamnidis May 9, 2025
41b0a22
Merge branch 'dev' into nf-test-minimal
TCLamnidis May 23, 2025
19529d3
move fastqc html to stable name
TCLamnidis May 23, 2025
8b28d79
Merge branch 'nf-test-minimal' of github.com:nf-core/eager into nf-te…
TCLamnidis May 23, 2025
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99 changes: 99 additions & 0 deletions tests/test_minimal.nf.test
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nextflow_pipeline {

name "Test pipeline: NFCORE_EAGER"
script "main.nf"
tag "pipeline"
tag "nfcore_eager"
tag "test_minimal"

test("test_minimal_profile") {

when {
params {
outdir = "$outputDir"
}
}

then {

///////////////////
// DOCUMENTATION //
///////////////////

// The contents of each top level results directory should be tested with individually named snapshots.
// Within each snapshot, there should be two to three distinct variables, that contain the files to be tested.
// - stable_name_<dir> is for files with variable md5sums (i.e. content) so only names will be compared
// - stable_content_<dir> is for files with stable md5sums (i.e. content) so md5sums will be compared
// - bams_<dir> is for BAM files, where the headerMD5 is checked for stability (since the content can be unstable)
// If a directory is fully stable, you can drop `stable_name_*`
// If a directory contains no BAMs, you can drop `bams_*`

// Generate with: nf-test test --tag test_minimal --profile docker,test_minimal --update-snapshot
// Test with: nf-test test --tag test_minimal --profile docker,test_minimal
// NOTE: BAMs are always only stable in name, because:
// a) sharding breaks header since the shard that was first is named in the header (Fixed in https://github.com/nf-core/eager/pull/1112)
// b) the order of the reads in the BAMs is not stable (sorted, but reads that share a start position can be in any order)
// point b) also causes BAIs to be unstable.
// c) Merging of multiple BAMs with duplicate @RG / @PG tags can cause the header to be unstable (particularly in the case of shards/lanes)

//////////////////////
// DEFINE VARIABLES //
//////////////////////

// Define exclusion patterns for files with unstable contents
// NOTE: When a section needs more than a couple of small patterns, consider adding a variable to store the patterns here
// This is particularly important if the patterns excluded in the stable content section should be included in the stable name section


// Check that no files are missing/added
// Command legend: Result directory to index , includeDir: include dirs?, ignore: exclude patterns , ignoreFile: exclude pattern list , include: include patterns
def stable_name_all = getAllFilesFromDir("$outputDir/" , includeDir: false , ignore: ['pipeline_info/*'] , ignoreFile: null , include: ['*', '**/*'] )

// Authentication
def stable_content_authentication = getAllFilesFromDir("$outputDir/authentication" , includeDir: false , ignore: null , ignoreFile: null , include: ['*', '**/*'] )
// def stable_name_authentication = getAllFilesFromDir("$outputDir/authentication" , includeDir: false , ignore: null , ignoreFile: null , include: unstable_patterns_auth)

// Final_bams
def stable_content_final_bams = getAllFilesFromDir("$outputDir/final_bams" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.flagstat'] )
def stable_name_final_bams = getAllFilesFromDir("$outputDir/final_bams" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )

// Mapping (incl. bam_input flasgstat)
def stable_content_mapping = getAllFilesFromDir("$outputDir/mapping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.flagstat'] )
def stable_name_mapping = getAllFilesFromDir("$outputDir/mapping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )

// Preprocessing
def stable_content_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , includeDir: false , ignore: ['**/*.{zip,html}'] , ignoreFile: null , include: ['**/*'] )
def stable_name_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{zip,html}'] )

// MultiQC
def stable_name_multiqc = getAllFilesFromDir("$outputDir/multiqc" , includeDir: false , ignore: null , ignoreFile: null , include: ['*', '**/*'] )

///////////////////////
// DEFINE ASSERTIONS //
///////////////////////

assertAll(
{ assert workflow.success },
// This checks that there are no missing or additional output files.
// Also a good starting point to look at all the files in the output folder than need to be checked in subsequent sections.
{ assert snapshot( stable_name_all*.name ).match("all_files") },

// Checking changes to contents of each section
// NOTE: Keep the order of the sections in the alphanumeric order of the output directories.
// Each section should first check stable_content, stable_name second (if applicable).
{ assert snapshot( stable_content_authentication ).match("authentication") },
{ assert snapshot( stable_content_final_bams , stable_name_final_bams*.name ).match("final_bams") },
// NOTE: The snapshot section for mapping cannot be named 'mapping'. See https://github.com/askimed/nf-test/issues/279
{ assert snapshot( stable_content_mapping , stable_name_mapping*.name ).match("mapping_output") },
{ assert snapshot( stable_content_preprocessing , stable_name_preprocessing*.name ).match("preprocessing") },

// MultiQC
{ assert snapshot( stable_name_multiqc*.name ).match("multiqc") },

// Versions
{ assert new File("$outputDir/pipeline_info/nf_core_eager_software_mqc_versions.yml").exists() },

)
}
}
}
249 changes: 249 additions & 0 deletions tests/test_minimal.nf.test.snap
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{
"all_files": {
"content": [
[
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_percent_on_target_mqc.json",
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_percent_on_target_mqc.json",
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_percent_on_target_mqc.json",
"JK2782_Mammoth_MT_Krause.bam",
"JK2782_Mammoth_MT_Krause.bam.bai",
"JK2802_Mammoth_MT_Krause.bam",
"JK2802_Mammoth_MT_Krause.bam.bai",
"JK2782_Mammoth_MT_Krause.flagstat",
"JK2802_Mammoth_MT_Krause.flagstat",
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_sorted.flagstat",
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_sorted.bam",
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_sorted.bam.bai",
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam",
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam.bai",
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam",
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam.bai",
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.flagstat",
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.flagstat",
"fastqc-status-check-heatmap.txt",
"fastqc_adapter_content_plot.txt",
"fastqc_per_base_n_content_plot.txt",
"fastqc_per_base_sequence_quality_plot.txt",
"fastqc_per_sequence_gc_content_plot_Counts.txt",
"fastqc_per_sequence_gc_content_plot_Percentages.txt",
"fastqc_per_sequence_quality_scores_plot.txt",
"fastqc_sequence_counts_plot.txt",
"fastqc_sequence_duplication_levels_plot.txt",
"fastqc_top_overrepresented_sequences_table.txt",
"multiqc.log",
"multiqc_citations.txt",
"multiqc_data.json",
"multiqc_fastqc.txt",
"multiqc_general_stats.txt",
"multiqc_samtools_flagstat.txt",
"multiqc_software_versions.txt",
"multiqc_sources.txt",
"samtools-flagstat-dp_Percentage_of_total.txt",
"samtools-flagstat-dp_Read_counts.txt",
"fastqc-status-check-heatmap.pdf",
"fastqc_adapter_content_plot.pdf",
"fastqc_per_base_n_content_plot.pdf",
"fastqc_per_base_sequence_quality_plot.pdf",
"fastqc_per_sequence_gc_content_plot_Counts.pdf",
"fastqc_per_sequence_gc_content_plot_Percentages.pdf",
"fastqc_per_sequence_quality_scores_plot.pdf",
"fastqc_sequence_counts_plot-cnt.pdf",
"fastqc_sequence_counts_plot-pct.pdf",
"fastqc_sequence_duplication_levels_plot.pdf",
"fastqc_top_overrepresented_sequences_table.pdf",
"general_stats_table.pdf",
"samtools-flagstat-dp_Percentage_of_total.pdf",
"samtools-flagstat-dp_Read_counts.pdf",
"fastqc-status-check-heatmap.png",
"fastqc_adapter_content_plot.png",
"fastqc_per_base_n_content_plot.png",
"fastqc_per_base_sequence_quality_plot.png",
"fastqc_per_sequence_gc_content_plot_Counts.png",
"fastqc_per_sequence_gc_content_plot_Percentages.png",
"fastqc_per_sequence_quality_scores_plot.png",
"fastqc_sequence_counts_plot-cnt.png",
"fastqc_sequence_counts_plot-pct.png",
"fastqc_sequence_duplication_levels_plot.png",
"fastqc_top_overrepresented_sequences_table.png",
"general_stats_table.png",
"samtools-flagstat-dp_Percentage_of_total.png",
"samtools-flagstat-dp_Read_counts.png",
"fastqc-status-check-heatmap.svg",
"fastqc_adapter_content_plot.svg",
"fastqc_per_base_n_content_plot.svg",
"fastqc_per_base_sequence_quality_plot.svg",
"fastqc_per_sequence_gc_content_plot_Counts.svg",
"fastqc_per_sequence_gc_content_plot_Percentages.svg",
"fastqc_per_sequence_quality_scores_plot.svg",
"fastqc_sequence_counts_plot-cnt.svg",
"fastqc_sequence_counts_plot-pct.svg",
"fastqc_sequence_duplication_levels_plot.svg",
"fastqc_top_overrepresented_sequences_table.svg",
"general_stats_table.svg",
"samtools-flagstat-dp_Percentage_of_total.svg",
"samtools-flagstat-dp_Read_counts.svg",
"multiqc_report.html",
"JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.html",
"JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.zip",
"JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.html",
"JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.zip",
"JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html",
"JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.zip"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.6"
},
"timestamp": "2025-05-23T10:36:48.672625"
},
"preprocessing": {
"content": [
[

],
[
"JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.html",
"JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.zip",
"JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.html",
"JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.zip",
"JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html",
"JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.zip"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.6"
},
"timestamp": "2025-05-23T10:36:48.803481"
},
"final_bams": {
"content": [
[
"JK2782_Mammoth_MT_Krause.flagstat:md5,9ebb4b5e99894d2a87ac3b60a78e7142",
"JK2802_Mammoth_MT_Krause.flagstat:md5,51816d63f34b4818ed6f1ec968f05fc0"
],
[
"JK2782_Mammoth_MT_Krause.bam",
"JK2782_Mammoth_MT_Krause.bam.bai",
"JK2802_Mammoth_MT_Krause.bam",
"JK2802_Mammoth_MT_Krause.bam.bai"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.6"
},
"timestamp": "2025-05-23T10:36:48.749353"
},
"multiqc": {
"content": [
[
"fastqc-status-check-heatmap.txt",
"fastqc_adapter_content_plot.txt",
"fastqc_per_base_n_content_plot.txt",
"fastqc_per_base_sequence_quality_plot.txt",
"fastqc_per_sequence_gc_content_plot_Counts.txt",
"fastqc_per_sequence_gc_content_plot_Percentages.txt",
"fastqc_per_sequence_quality_scores_plot.txt",
"fastqc_sequence_counts_plot.txt",
"fastqc_sequence_duplication_levels_plot.txt",
"fastqc_top_overrepresented_sequences_table.txt",
"multiqc.log",
"multiqc_citations.txt",
"multiqc_data.json",
"multiqc_fastqc.txt",
"multiqc_general_stats.txt",
"multiqc_samtools_flagstat.txt",
"multiqc_software_versions.txt",
"multiqc_sources.txt",
"samtools-flagstat-dp_Percentage_of_total.txt",
"samtools-flagstat-dp_Read_counts.txt",
"fastqc-status-check-heatmap.pdf",
"fastqc_adapter_content_plot.pdf",
"fastqc_per_base_n_content_plot.pdf",
"fastqc_per_base_sequence_quality_plot.pdf",
"fastqc_per_sequence_gc_content_plot_Counts.pdf",
"fastqc_per_sequence_gc_content_plot_Percentages.pdf",
"fastqc_per_sequence_quality_scores_plot.pdf",
"fastqc_sequence_counts_plot-cnt.pdf",
"fastqc_sequence_counts_plot-pct.pdf",
"fastqc_sequence_duplication_levels_plot.pdf",
"fastqc_top_overrepresented_sequences_table.pdf",
"general_stats_table.pdf",
"samtools-flagstat-dp_Percentage_of_total.pdf",
"samtools-flagstat-dp_Read_counts.pdf",
"fastqc-status-check-heatmap.png",
"fastqc_adapter_content_plot.png",
"fastqc_per_base_n_content_plot.png",
"fastqc_per_base_sequence_quality_plot.png",
"fastqc_per_sequence_gc_content_plot_Counts.png",
"fastqc_per_sequence_gc_content_plot_Percentages.png",
"fastqc_per_sequence_quality_scores_plot.png",
"fastqc_sequence_counts_plot-cnt.png",
"fastqc_sequence_counts_plot-pct.png",
"fastqc_sequence_duplication_levels_plot.png",
"fastqc_top_overrepresented_sequences_table.png",
"general_stats_table.png",
"samtools-flagstat-dp_Percentage_of_total.png",
"samtools-flagstat-dp_Read_counts.png",
"fastqc-status-check-heatmap.svg",
"fastqc_adapter_content_plot.svg",
"fastqc_per_base_n_content_plot.svg",
"fastqc_per_base_sequence_quality_plot.svg",
"fastqc_per_sequence_gc_content_plot_Counts.svg",
"fastqc_per_sequence_gc_content_plot_Percentages.svg",
"fastqc_per_sequence_quality_scores_plot.svg",
"fastqc_sequence_counts_plot-cnt.svg",
"fastqc_sequence_counts_plot-pct.svg",
"fastqc_sequence_duplication_levels_plot.svg",
"fastqc_top_overrepresented_sequences_table.svg",
"general_stats_table.svg",
"samtools-flagstat-dp_Percentage_of_total.svg",
"samtools-flagstat-dp_Read_counts.svg",
"multiqc_report.html"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.6"
},
"timestamp": "2025-05-23T10:36:48.824552"
},
"mapping_output": {
"content": [
[
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_sorted.flagstat:md5,9a10991f5670a52975a622a8b056e2bc",
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.flagstat:md5,274942e6f459e1f85bffd0719ea24038",
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.flagstat:md5,51816d63f34b4818ed6f1ec968f05fc0"
],
[
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_sorted.bam",
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_sorted.bam.bai",
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam",
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam.bai",
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam",
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam.bai"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.6"
},
"timestamp": "2025-05-23T10:36:48.771636"
},
"authentication": {
"content": [
[
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_percent_on_target_mqc.json:md5,13303511f19f618a524e30b3377497fb",
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_percent_on_target_mqc.json:md5,90a8f1d5c1017f0000ac960b03767eba",
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_percent_on_target_mqc.json:md5,d26aac162887528fb3a3b2fa9b86954f"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.6"
},
"timestamp": "2025-05-23T10:36:48.717265"
}
}