LongRead Quality Control and Filtering
Version 1

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Workflow Type: Common Workflow Language

Work-in-progress

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

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SEEK ID: https://workflowhub.eu/workflows/337?version=1

Inputs

ID	Name	Description	Type
identifier	identifier used	Identifier for this dataset used in this workflow	string
nanopore_reads	Nanopore reads	Nanopore sequence file locally fastq format	File[]
filter_references	Contamination reference file	Contamination references fasta file for contamination filtering	File[]?
keep_reference_mapped_reads	Keep mapped reads	Keep with reads mapped to the given reference	boolean
kraken_database	Kraken2 database	Kraken2 database location, multiple databases is possible	Directory[]?
threads	Number of threads	Number of threads to use for computational processes	int?
memory	Maximum memory in MB	Maximum memory usage in megabytes	int?
step	CWL base step number	Step number for order of steps	int?
destination	Output Destination	Optional Output destination used for cwl-prov reporting.	string?

ID	Name	Description
merge_nanopore_fastq	Merge fastq files	n/a
fastqc_nanopore_before	FastQC before	Quality assessment and report of reads before filter
prepare_bbmap_db	Prepare references	Prepare BBMap references to a single fasta file and unique headers
nanopore_array_to_file	array to file	Converts the file array to a single file object
nanopore_quality_kraken2	Kraken2	Taxonomic classification of FASTQ reads
nanopore_quality_kraken2_krona	Krona	Visualization of Kraken2 classification with Krona
reference_filter_nanopore	Reference mapping	Removal of contaminated reads using minimap2 mapping
fastqc_nanopore_after	FastQC after	Quality assessment and report of reads before filter
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
filtered_reads	Filtered nanopore reads	Filtered nanopore reads	File