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jbv2jbv2
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‎tests/test_humanpopgen.nf.test‎

Lines changed: 12 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -70,6 +70,10 @@ nextflow_pipeline {
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def stable_content_authentication = getAllFilesFromDir("$outputDir/authentication" , includeDir: false , ignore: unstable_patterns_auth , ignoreFile: null , include: ['*', '**/*'] )
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def stable_name_authentication = getAllFilesFromDir("$outputDir/authentication" , includeDir: false , ignore: null , ignoreFile: null , include: unstable_patterns_auth)
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// Damage manipulation
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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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// Deduplication - TODO -> snapshot both lists are empty!?
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def stable_content_deduplication = getAllFilesFromDir("$outputDir/deduplication" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.flagstat'] )
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def stable_name_deduplication = getAllFilesFromDir("$outputDir/deduplication" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
@@ -78,10 +82,18 @@ nextflow_pipeline {
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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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// Genotyping
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def stable_content_genotyping = getAllFilesFromDir("$outputDir/genotyping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*'] )
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def stable_name_genotyping = getAllFilesFromDir("$outputDir/genotyping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.tbi'] )
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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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// Metagenomics
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def stable_content_metagenomics = getAllFilesFromDir("$outputDir/metagenomics" , includeDir: false , ignore: ['**/*.biom', '**/*table.tsv'] , ignoreFile: null , include: ['**/*'] )
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def stable_name_metagenomics = getAllFilesFromDir("$outputDir/metagenomics" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.biom', '**/*table.tsv'] )
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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("$outputDir/preprocessing" , includeDir: false , ignore: ['**/*.{zip,log,html}'], ignoreFile: null , include: ['**/*'] )
@@ -91,18 +103,6 @@ nextflow_pipeline {
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def stable_content_readfiltering = getAllFilesFromDir("$outputDir/read_filtering" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.flagstat'] )
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def stable_name_readfiltering = getAllFilesFromDir("$outputDir/read_filtering" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
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// Genotyping
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def stable_content_genotyping = getAllFilesFromDir("$outputDir/genotyping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*'] )
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def stable_name_genotyping = getAllFilesFromDir("$outputDir/genotyping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.tbi'] )
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// Metagenomics
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def stable_content_metagenomics = getAllFilesFromDir("$outputDir/metagenomics" , includeDir: false , ignore: ['**/*.biom', '**/*table.tsv'] , ignoreFile: null , include: ['**/*'] )
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def stable_name_metagenomics = getAllFilesFromDir("$outputDir/metagenomics" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.biom', '**/*table.tsv'] )
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// Damage manipulation
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def stable_content_damage_manipulation = getAllFilesFromDir("$outputDir/damage_manipulation" , includeDir: false , ignore: unstable_patterns_auth , ignoreFile: null , include: ['*', '**/*'] )
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def stable_name_damage_manipulation = getAllFilesFromDir("$outputDir/damage_manipulation" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
105-
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// Samtools
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def stable_content_samtools = getAllFilesFromDir("$outputDir/samtools" , includeDir: false , ignore: unstable_patterns_auth , ignoreFile: null , include: ['*', '**/*'] )
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def stable_name_samtools = getAllFilesFromDir("$outputDir/samtools" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
@@ -130,7 +130,6 @@ nextflow_pipeline {
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{ assert snapshot( stable_content_genotyping , stable_name_genotyping*.name ).match("genotyping") },
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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_mapstats , stable_name_mapstats*.name ).match("mapstats") },
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{ assert snapshot( stable_content_metagenomics , stable_name_metagenomics*.name ).match("metagenomics") },
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{ assert snapshot( stable_content_preprocessing , stable_name_preprocessing*.name ).match("preprocessing") },
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{ assert snapshot( stable_content_readfiltering , stable_name_readfiltering*.name ).match("read_filtering") },

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