Read quality control, trimming and contamination filter.

Workflow for (paired) read quality control, trimming and contamination filtering based on a given reference.

Will output a merged set of read pairs, when multiple datasets are used.

Steps:

Inputs

ID	Name	Description	Type
identifier	identifier used	Identifier for this dataset used in this workflow	string
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	filter rRNA	Optionally remove rRNA sequences from the reads.	boolean
forward_reads	forward reads	forward sequence file locally	File[]
reverse_reads	reverse reads	reverse sequence file locally	File[]
bbmap_reference	contamination reference file	bbmap reference fasta file for contamination filtering	string
step	CWL base step number	Step number for order of steps	int?

Steps

ID	Name	Description
fastqc	FastQC	Quality assessment and report of reads
fastq_merge_fwd	fastq pair merge file	Merge multiple paired ends of fastq files
fastq_merge_rev	fastq pair merge file	Merge multiple paired ends of fastq files
fastp	fastp	Read quality filtering and (barcode) trimming.
bbmap_contamination	contamination filter (bbmap)	Filters contamination sequences from reads using bbmap
bbduk_rrna	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
bbmap_files_to_folder	contamination output	Preparation of contamination-filter (bbduk) output files to a specific output folder. Contains fwd/rev reads stats and summary file.
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.

Outputs

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. (this output is mainly used for other workflows)	File
QC_reverse_reads	Filtered reverse read	Filtered reverse read with fastp and (optionally) rrna filtered. (this output is mainly used for other workflows)	File

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Read quality control, trimming and contamination filter.
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