Skip to content

Commit

Permalink
add command legend, and align a bit more
Browse files Browse the repository at this point in the history
  • Loading branch information
@TCLamnidis
TCLamnidis committed Dec 20, 2024
1 parent 53d82b0 commit 5ed2b0b
Showing 1 changed file with 21 additions and 19 deletions.
40 changes: 21 additions & 19 deletions tests/test.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -28,42 +28,44 @@ nextflow_pipeline {
// 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.

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

//Bam filtering
def stable_content_bamfiltering = getAllFilesFromDir("$outputDir/bam_filtering" , true , ['*.{bam,bai}'] , null , ['*.flagstat'] )
def stable_name_bamfiltering = getAllFilesFromDir("$outputDir/bam_filtering" , true , ['*.flagstat'] , null , ['*.{bam,bai}'] )
// Bam filtering
def stable_content_bamfiltering = getAllFilesFromDir("$outputDir/bam_filtering" , true , ['*.{bam,bai}'] , null , ['*.flagstat'] )
def stable_name_bamfiltering = getAllFilesFromDir("$outputDir/bam_filtering" , true , ['*.flagstat'] , null , ['*.{bam,bai}'] )

// Bam input stats
def stable_content_baminputstats = getAllFilesFromDir("$outputDir/bam_input_stats" , true , null , null , ['*.flagstat'] )
def stable_content_baminputstats = getAllFilesFromDir("$outputDir/bam_input_stats" , true , null , null , ['*.flagstat'] )

// Damage estimation
def stable_content_damageestimation = getAllFilesFromDir("$outputDir/damage_estimation" , true , ['**/*.{svg,pdf,log}'] , null , ['**/*.{txt,json}'] )
def stable_name_damageestimation = getAllFilesFromDir("$outputDir/damage_estimation" , true , ['**/*.{txt,json}'] , null , ['**/*.{svg,pdf,log}'] )
def stable_content_damageestimation = getAllFilesFromDir("$outputDir/damage_estimation" , true , ['**/*.{svg,pdf,log}'] , null , ['**/*.{txt,json}'] )
def stable_name_damageestimation = getAllFilesFromDir("$outputDir/damage_estimation" , true , ['**/*.{txt,json}'] , null , ['**/*.{svg,pdf,log}'] )

// Deduplication
def stable_content_deduplication = getAllFilesFromDir("$outputDir/deduplication" , true , ['*.{bam,bai}'] , null , ['*.flagstat'] )
def stable_name_deduplication = getAllFilesFromDir("$outputDir/deduplication" , true , ['*.flagstat'] , null , ['*.{bam,bai}'] )
def stable_content_deduplication = getAllFilesFromDir("$outputDir/deduplication" , true , ['*.{bam,bai}'] , null , ['*.flagstat'] )
def stable_name_deduplication = getAllFilesFromDir("$outputDir/deduplication" , true , ['*.flagstat'] , null , ['*.{bam,bai}'] )

// Final_bams
def stable_content_final_bams = getAllFilesFromDir("$outputDir/final_bams" , true , null , null , ['**/*.flagstat'] )
def stable_name_final_bams = getAllFilesFromDir("$outputDir/final_bams" , true , null , null , ['**/*.{bam,bai}'] )
def stable_content_final_bams = getAllFilesFromDir("$outputDir/final_bams" , true , null , null , ['**/*.flagstat'] )
def stable_name_final_bams = getAllFilesFromDir("$outputDir/final_bams" , true , null , null , ['**/*.{bam,bai}'] )

//Mapping
def stable_content_mapping = getAllFilesFromDir("$outputDir/mapping" , true , null , null , ['**/*.flagstat'] )
def stable_name_mapping = getAllFilesFromDir("$outputDir/mapping" , true , null , null , ['**/*.{bam,bai}'] )
// Mapping
def stable_content_mapping = getAllFilesFromDir("$outputDir/mapping" , true , null , null , ['**/*.flagstat'] )
def stable_name_mapping = getAllFilesFromDir("$outputDir/mapping" , true , null , null , ['**/*.{bam,bai}'] )

// Mapstats
// NOTE: GC content data and plot has minor changes between runs. I suspect this is because of the order of reads that start at the same position being unstable, but I am not sure.
def stable_content_mapstats = getAllFilesFromDir("$outputDir/mapstats" , true , ['**/*.html', '**/mapped_reads_gc-content_distribution.txt', '**/genome_gc_content_per_window.png'], null , ['**/*.{bed,json,txt,log,css,png,js}'] )
def stable_name_mapstats = getAllFilesFromDir("$outputDir/mapstats" , true , null , null , ['**/*.html', '**/mapped_reads_gc-content_distribution.txt', '**/genome_gc_content_per_window.png'] )
def stable_content_mapstats = getAllFilesFromDir("$outputDir/mapstats" , true , ['**/*.html', '**/mapped_reads_gc-content_distribution.txt', '**/genome_gc_content_per_window.png'], null , ['**/*.{bed,json,txt,log,css,png,js}'] )
def stable_name_mapstats = getAllFilesFromDir("$outputDir/mapstats" , true , null , null , ['**/*.html', '**/mapped_reads_gc-content_distribution.txt', '**/genome_gc_content_per_window.png'] )

// MultiQC
def stable_name_multiqc = getAllFilesFromDir("$outputDir/multiqc" , true , null , null , ['*', '**/*'] )
def stable_name_multiqc = getAllFilesFromDir("$outputDir/multiqc" , true , null , null , ['*', '**/*'] )

// Preprocessing
def stable_content_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , true , ['**/*.{zip,log}', '**/*fastp.html'], null , ['**/*'] )
def stable_name_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , true , null , null , ['**/*.{zip,log}', '**/*fastp.html'] )
def stable_content_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , true , ['**/*.{zip,log}', '**/*fastp.html'], null , ['**/*'] )
def stable_name_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , true , null , null , ['**/*.{zip,log}', '**/*fastp.html'] )

assertAll(
{ assert workflow.success },
Expand Down

0 comments on commit 5ed2b0b

Please sign in to comment.