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FastQC Pipeline

A straightforward program which can take a file list of fastq's, concatenate them, and perform FastQC on them in serial or scalable parallel

Requirements

Python - built on 3.10x but should be fine for the forseeable future
FastQC - the underlying tool to perform QC on your read files
Bash Environment - current mechanics rely on system calls to the bash command line

Input File

File structure should follow the convention SampleID_Lane#_Read#.fastq. For example: Exp001_S1_L002_R1_001.fastq

FastQC Pipe expects a tab-delimited text file with the following structure (lines led with '#' are ignored):

Path/of/directory | Sample_Name | R1/2/Both

Example:

/home/RPINerd/M01234/Fastq_Generation Exp001_S1   2
/home/RPINerd/M01234/Fastq_Generation Exp001_S2   1
/home/RPINerd/M01234/Fastq_Generation Exp001_S3   Both

Running Pipeline

General format for run is python3 fastqc_pipe.py -f file_list.tsv

The input file is the only required argument however there are some additional options:
--threads or -t # specifies how many threads to allocate to the fastqc algorithm, currently capped at 12
--merge or -m <desired/path/to/> allows for a preferred location to be specified for the merged lanes to be written to
--verbose or -v pumps out a ton of extra info and saves it to the file fastqc_pipe.log