Workflow for Illumina Quality Control and Filtering
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Workflow Type: Common Workflow Language

Stable

Workflow for Illumina Quality Control and Filtering

Multiple paired datasets will be merged into single paired dataset.

Summary:

FastQC on raw data files
fastp for read quality trimming
BBduk for phiX and (optional) rRNA filtering
Kraken2 for taxonomic classification of reads (optional)
BBmap for (contamination) filtering using given references (optional)
FastQC on filtered (merged) data

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

All tool CWL files and other workflows can be found here:
https://gitlab.com/m-unlock/cwl

How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html

Click and drag the diagram to pan, double click or use the controls to zoom.

SEEK ID: https://workflowhub.eu/workflows/336?version=1

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 in MB	Maximum memory usage in MegaBytes	int?
forward_reads	Forward reads	Forward sequence fastq file(s) locally	File[]
reverse_reads	Reverse reads	Reverse sequence fastq file(s) locally	File[]
skip_qc_unfiltered	Skip QC unfiltered	Skip FastQC analyses of raw input reads (default false)	boolean?
skip_qc_filtered	Skip QC filtered	Skip FastQC analyses of filtered input reads (default false)	boolean?
filter_rrna	filter rRNA	Optionally remove rRNA sequences from the reads (default false)	boolean?
filter_references	Filter reference file(s)	References fasta file(s) for filtering	File[]?
deduplicate	Deduplicate reads	Remove exact duplicate reads with fastp	boolean?
kraken2_confidence	Kraken2 confidence threshold	Confidence score threshold (default 0.0) must be between [0, 1]	float?
kraken2_database	Kraken2 database	Kraken2 database location, multiple databases is possible	Directory[]?
kraken2_standard_report	Kraken2 standard report	Also output Kraken2 standard report with per read classification. These can be large. (default false)	boolean
keep_reference_mapped_reads	Keep mapped reads	Keep with reads mapped to the given reference (default false)	boolean?
prepare_reference	Prepare references	Prepare references to a single fasta file and unique headers (default true). When false a single fasta file as reference is expected with unique headers	boolean
step	Output Step number	Step number for output folder numbering (default 1)	int?
destination	Output Destination	Optional output destination only used for cwl-prov reporting.	string?

Steps

ID	Name	Description
fastqc_illumina_before	FastQC before	Quality assessment and report of reads
fastq_merge_fwd	Merge forward reads	Merge multiple forward fastq reads to a single file
fastq_merge_rev	Merge reverse reads	Merge multiple reverse fastq reads to a single file
fastq_fwd_array_to_file	Fwd reads array to file	Forward file of single file array to file object
fastq_rev_array_to_file	Rev reads array to file	Forward file of single file array to file object
fastp	fastp	Read quality filtering and (barcode) trimming.
rrna_filter	rRNA filter (bbduk)	Filters rRNA sequences from reads using bbduk
reference_array_to_file	Reference array to file	Array to file object when the reference does not need to be prepared
prepare_fasta_db	Prepare references	Prepare references to a single fasta file and unique headers
reference_filter_illumina	Reference read mapping	Map reads against references using BBMap
phix_filter	PhiX filter (bbduk)	Filters illumina spike-in PhiX sequences from reads using bbduk
illumina_kraken2_unfiltered	Kraken2 unfiltered	Taxonomic classification on unfiltered files
illumina_kraken2_filtered	Kraken2 unfiltered	Taxonomic classification on unfiltered files
illumina_kraken2_compress	Compress kraken2	Compress large kraken2 report file
illumina_kraken2_krona	Krona Kraken2	Visualization of kraken2 with Krona
fastqc_illumina_after	FastQC after	Quality assessment and report of reads
reports_files_to_folder	Reports to folder	Preparation of fastp output files to a specific output folder
kraken2_files_to_folder	Kraken2 folder	Kraken2 files to single folder

Outputs

ID	Name	Description	Type
reports_folder	Filtering reports folder	Folder containing all reports of filtering and quality control	Directory
kraken2_folder	Kraken2 folder	Folder with Kraken2 output files	Directory?
QC_forward_reads	Filtered forward read	Filtered forward read	File
QC_reverse_reads	Filtered reverse read	Filtered reverse read	File