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TCLamnidisTCLamnidis
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harshil align
1 parent a464f53 commit efb173a

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Lines changed: 22 additions & 22 deletions

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‎tests/test_humanpopgen.nf.test‎

Lines changed: 22 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -63,48 +63,48 @@ nextflow_pipeline {
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]
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// Check that no files are missing/added
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// Command legend: Result directory to index , includeDir: include dirs?, ignore: exclude patterns , ignoreFile: exclude pattern list , include: include patterns
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def stable_name_all = getAllFilesFromDir("$outputDir/" , includeDir: false , ignore: ['pipeline_info/*'] , ignoreFile: null , include: ['*', '**/*'] )
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// Command legend: Result directory to index , includeDir: include dirs? , ignore: exclude patterns , ignoreFile: exclude pattern list , include: include patterns
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def stable_name_all = getAllFilesFromDir("$outputDir/" , includeDir: false , ignore: ['pipeline_info/*'] , ignoreFile: null , include: ['*', '**/*'] )
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// Authentication
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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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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("$outputDir/damage_manipulation" , includeDir: false , ignore: ['**/*.{bam,bai}'] , ignoreFile: null , include: ['*', '**/*'] )
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def stable_name_damage_manipulation = getAllFilesFromDir("$outputDir/damage_manipulation" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
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def stable_content_damage_manipulation = getAllFilesFromDir("$outputDir/damage_manipulation" , includeDir: false , ignore: ['**/*.{bam,bai}'] , ignoreFile: null , include: ['*', '**/*'] )
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def stable_name_damage_manipulation = getAllFilesFromDir("$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}'] )
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// Deduplication
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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}'] )
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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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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("$outputDir/genotyping" , includeDir: false , ignore: ['**/*.{geno,ind,snp,tsv}'] , ignoreFile: null , include: ['**/*'] )
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def stable_name_genotyping = getAllFilesFromDir("$outputDir/genotyping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{geno,ind,snp,tsv}'] )
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def stable_content_genotyping = getAllFilesFromDir("$outputDir/genotyping" , includeDir: false , ignore: ['**/*.{geno,ind,snp,tsv}'] , ignoreFile: null , include: ['**/*'] )
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def stable_name_genotyping = getAllFilesFromDir("$outputDir/genotyping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{geno,ind,snp,tsv}'] )
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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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// 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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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("$outputDir/preprocessing" , includeDir: false , ignore: ['**/*.{zip,log,html}'], ignoreFile: null , include: ['**/*'] )
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def stable_name_preprocessing = getAllFilesFromDir("$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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// Read filtering
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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}'] )
103+
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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// MultiQC
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def stable_name_multiqc = getAllFilesFromDir("$outputDir/multiqc" , includeDir: false , ignore: null , ignoreFile: null , include: ['*', '**/*'] )
107+
def stable_name_multiqc = getAllFilesFromDir("$outputDir/multiqc" , includeDir: false , ignore: null , ignoreFile: null , include: ['*', '**/*'] )
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///////////////////////
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// DEFINE ASSERTIONS //

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