Read quality control and trimming
Version 1

Work-in-progress

Workflow for read quality control and trimming.

Steps:

- FastQC (read quality control)

- fastp (read quality trimming)

- bbduk used for rrna filtering

SEEK ID: https://workflowhub.eu/workflows/96?version=1

Inputs

ID	Name	Description	Type
threads	number of threads	number of threads to use for computational processes	int?
memory	maximum memory usage in megabytes	maximum memory usage in megabytes	int?
filter_rrna	n/a	n/a	boolean
forward_reads	forward reads	forward sequence file locally	File
reverse_reads	reverse reads	reverse sequence file locally	File
step	CWL base step number	Step number for order of steps	int?

ID	Name	Description
fastqc	FastQC	Quality assessment and report of reads
fastp	fastp	Read quality filtering and (barcode) trimming.
bbduk	rrna filter (bbduk)	Filters rrna sequences from reads using bbduk
fastqc_files_to_folder	FastQC output	Preparation of FastQC output files to a specific output folder
filtered_files_to_folder	fastp output	Preparation of fastp output files to a specific output folder
bbduk_files_to_folder	fastp output	Preparation of rrna-filter (bbduk) output files to a specific output folder. Contains fwd/rev reads stats and summary file.

ID	Name	Description	Type
files_to_folder_fastqc	FASTQC	Quality reporting by FASTQC	Directory
files_to_folder_filtered	Filtered reads folder	Output folder with filtered reads, stats and reports.	Directory
QC_forward_reads	Filtered forward read	Filtered forward read with fastp and (optionally) rrna filtered.	File
QC_reverse_reads	Filtered reverse read	Filtered reverse read with fastp and (optionally) rrna filtered.	File