fastq_QC_processing

Nextflow pipeline to analyze and modify fastq sequence quality

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Workflow overview

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Input

• Directory path with .fastq.gz sequences

• Output directory path

Output

• Main output: PDF Trim report

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Requirements

Compatible OS*:

• Ubuntu 20.04 LTS
• Ubuntu 18.04 LTS

Software

Requierment	Version	Required Commands *
Java	v11.0.11	java
Nextflow	21.10.5	nextflow run
Trimmomatic	v0.39	java -jar ILLUMINACLIP, AVGQUAL, LEADING, TRAILING, SLIDINGWINDOW, MINLEN
Fastqc	v0.11.9	fastqc
Plan9port	Latest (as of 10/01/2019 )	mk **
R	v 4.1.2	Rscript
pandoc	2.5	pandoc
pdfLatex	-	compiling LaTeX into PDF

• These commands must be accessible from your $PATH (i.e. you should be able to invoke them from your command line). ** Plan9 port builds many binaries, but you ONLY need the mk utility to be accessible from your command line.

R packages requierments

R package	Function
rmarkdown	render
dplyr	magrittr, filter(), mutate(), select(), arrange()
knitr	kable
kableExtra	kable_styling
tidyr	pivot_longer()
scales	colour pallettes
ggplot2	geom_col( ), ggplot()
vroom	vroom ()
cowplot	theme_cowplot()

Installation

Download fastq_QC_processing from Github repository:

git clone https://github.com/Iaguilaror/fastq_QC_processing.git

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Test

To test fastq_QC_processing execution using test data, run:

./runtest.sh 

Your console should print the Nextflow log for the run, once every process has been submitted, the following message will appear:

 ======
 Basic pipeline TEST SUCCESSFUL
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results for test data should be in the following directory:

./fastq_QC_processing/test/results/fastq_quality_control-results

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Usage

To run with your own data go to the pipeline directory and execute:

nextflow run fastq_quality_control.nf \
--input_dir $your_input_dir \
--output_dir $your_output_directory \
-resume \
-with-report $your_output_directory/`date +%Y%m%d_%H%M%S`_report.html \
-with-dag $your_output_directory/`date +%Y%m%d_%H%M%S`.DAG.html  

Important

Params for trimming must be modified in the nextflow.config file

• Meaning: trim_avgqual, trim_leading, trim_trailing, etcetera.

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For information about options and parameters, run:

nextflow run fastq_quality_control.nf --help

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Authors

Israel Aguilar Ordoñez