Workflow for Illumina Quality Control and Filtering
Version 1

Visit source

Workflow Type: Common Workflow Language

Stable

Multiple paired datasets will be merged into single paired dataset.

Summary:

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

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?
filter_rrna	filter rRNA	Optionally remove rRNA sequences from the reads.	boolean
forward_reads	Forward reads	Forward sequence fastq file(s) locally	File[]
reverse_reads	Reverse reads	Reverse sequence fastq file(s) locally	File[]
filter_references	Filter reference file(s)	References fasta file(s) for filtering	File[]?
deduplicate	Deduplicate reads	Remove exact duplicate reads with fastp	boolean?
kraken_database	Kraken2 database	Kraken2 database location, multiple databases is possible	Directory[]?
keep_reference_mapped_reads	Keep mapped reads	Keep with reads mapped to the given reference	boolean
step	Output Step number	Step number for output folder numbering	int?
destination	Output Destination	Optional Output destination used for cwl-prov reporting.	string?

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
fastp	fastp	Read quality filtering and (barcode) trimming.
rrna_filter	rRNA filter (bbduk)	Filters rRNA sequences from reads using bbduk
phix_filter	PhiX filter (bbduk)	Filters illumina spike-in PhiX sequences from reads using bbduk
illumina_quality_kraken2	Kraken2	Taxonomic classification of FASTQ reads
illumina_quality_kraken2_krona	Krona	Visualization of Kraken2 classification with Krona
prepare_bbmap_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
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

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