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jbv2jbv2
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ignoring and including damage manipulation csvs
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Lines changed: 10 additions & 11 deletions

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‎tests/test_long.nf.test‎

Lines changed: 10 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -29,8 +29,8 @@ nextflow_pipeline {
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// If a directory is fully stable, you can drop `stable_name_*`
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// If a directory contains no BAMs, you can drop `bams_*`
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32-
// Generate with: nf-test test --profile +docker --tag test --update-snapshot
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// Test with: nf-test test --profile +docker --tag test
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// Generate with: nf-test test --profile +docker --tag test_long --update-snapshot
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// Test with: nf-test test --profile +docker --tag test_long
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// NOTE: BAMs are always only stable in name, because:
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// 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)
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// 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)
@@ -57,7 +57,6 @@ nextflow_pipeline {
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'**/misincorporation.txt',
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'**/genome_results.txt',
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'**/*command.log',
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'**/*out_MCMC_*.csv',
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]
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// Check that no files are missing/added
@@ -70,21 +69,21 @@ nextflow_pipeline {
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// Damage_manipulation
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// def stable_content_damage_manipulation = getAllFilesFromDir("$outputDir/damage_manipulation" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*csv'] )
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def stable_content_damage_manipulation = getAllFilesFromDir("$outputDir/damage_manipulation" , includeDir: false , ignore: unstable_patterns_auth , ignoreFile: null , include: ['*', '**/*'] )
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def stable_name_damage_manipulation = getAllFilesFromDir("$outputDir/damage_manipulation" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
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def stable_content_damage_manipulation = getAllFilesFromDir("$outputDir/damage_manipulation" , includeDir: false , ignore: ['**/*out_MCMC_*.csv'], ignoreFile: null , include: ['*', '**/*'] )
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def stable_name_damage_manipulation = getAllFilesFromDir("$outputDir/damage_manipulation" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai,csv}'] )
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// Final_bams
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def stable_content_final_bams = getAllFilesFromDir("$outputDir/final_bams" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.flagstat'] )
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def stable_name_final_bams = getAllFilesFromDir("$outputDir/final_bams" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
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// // Mapping (incl. bam_input flasgstat)
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// def stable_content_mapping = getAllFilesFromDir("$outputDir/mapping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.flagstat'] )
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// def stable_name_mapping = getAllFilesFromDir("$outputDir/mapping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
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def stable_content_mapping = getAllFilesFromDir("$outputDir/mapping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.flagstat'] )
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def stable_name_mapping = getAllFilesFromDir("$outputDir/mapping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
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// // Preprocessing
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// // NOTE: FastQC html appears stable, but I worry it might just include a day timestamp instead of a full timestamp. To keep the expression simpler I removed both from checksum testing.
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// def stable_content_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , includeDir: false , ignore: ['**/*.{zip,log,html}'], ignoreFile: null , include: ['**/*'] )
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// def stable_name_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{zip,log,html}'] )
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def stable_content_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , includeDir: false , ignore: ['**/*.{zip,log,html}'], ignoreFile: null , include: ['**/*'] )
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def stable_name_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{zip,log,html}'] )
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// Genotyping
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def stable_content_genotyping = getAllFilesFromDir("$outputDir/genotyping" , includeDir: false , ignore: ['**/*.{tbi,vcf.gz}'] , ignoreFile: null , include: ['**/*'] )
@@ -112,8 +111,8 @@ nextflow_pipeline {
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{ assert snapshot( stable_content_damage_manipulation , stable_name_damage_manipulation*.name ).match("damage_manipulation") },
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{ assert snapshot( stable_content_final_bams , stable_name_final_bams*.name ).match("final_bams") },
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// NOTE: The snapshot section for mapping cannot be named 'mapping'. See https://github.com/askimed/nf-test/issues/279
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// { assert snapshot( stable_content_mapping , stable_name_mapping*.name ).match("mapping_output") },
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//{ assert snapshot( stable_content_preprocessing , stable_name_preprocessing*.name ).match("preprocessing") },
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{ assert snapshot( stable_content_mapping , stable_name_mapping*.name ).match("mapping_output") },
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{ assert snapshot( stable_content_preprocessing , stable_name_preprocessing*.name ).match("preprocessing") },
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{ assert snapshot( stable_content_genotyping , stable_name_genotyping*.name ).match("genotyping") },
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// Additional checks on the genotyping VCFs for content. Specifically the md5sums of the header FORMAT, INFO, FILTER, CONTIG lines, and sample names
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{ assert snapshot(

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