Nanopore Quality Control and Filtering
Version 1

Workflow Type: Common Workflow Language

Workflow for nanopore read quality control and contamination filtering.

  • FastQC before filtering (read quality control)
  • Kraken2 taxonomic read classification
  • Minimap2 read filtering based on given references
  • FastQC after filtering (read quality control)

All tool CWL files and other workflows can be found here:



ID Name Description Type
identifier identifier used Identifier for this dataset used in this workflow
  • string
reads Forward reads Forward sequence file locally
  • string[]
filter_references Contamination reference file Contamination references fasta file for contamination filtering
  • string[]
keep_reference_mapped_reads Keep mapped reads Keep with reads mapped to the given reference
  • boolean
run_kraken2 Kraken2 Optionally run kraken2 contamination inspection
  • boolean?
kraken_database Kraken2 database Kraken2 database location
  • 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?
step CWL base step number Step number for order of steps
  • int?


ID Name Description
merge_nanopore_fastq Merge fastq files n/a
fastqc_nanopore_before FastQC before Quality assessment and report of reads before filter
combine_references Combine references n/a
workflow_nanopore_kraken2 Kraken2 Taxonomic classification of FASTQ reads
workflow_krona Krona visualization of taxonomic 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

Version History

Version 1 (earliest) Created 21st Apr 2022 at 17:19 by Bart Nijsse

Initial commit

Open master 738cb87
help Creators and Submitter
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Views: 318

Created: 21st Apr 2022 at 17:19

Last updated: 21st Apr 2022 at 17:20

Last used: 7th Oct 2022 at 10:55

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Total size: 6.48 KB
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