Illumina read quality control, trimming and contamination filter.
Version 1

Workflow Type: Common Workflow Language

Workflow for Illumina paired read quality control, trimming and filtering.
Multiple paired datasets will be merged into single paired dataset.

  • 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

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
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
  • string[]
reverse_reads Reverse reads Reverse sequence fastq file(s) locally
  • string[]
filter_references Filter reference file(s) References fasta file(s) for filtering
  • string[]?
deduplicate Deduplicate reads Remove exact duplicate reads with fastp
  • boolean?
kraken_database Kraken2 database Kraken2 database location
  • string[]?
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?


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
combine_references Combine references Combine references to a single fasta file
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
destination Output Destination Optional Output destination used for cwl-prov reporting.
  • string?

Version History

Version 1 (earliest) Created 21st Apr 2022 at 14:00 by Bart Nijsse

Initial commit

Open master 799773f
help Creators and Submitter
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Views: 380

Created: 21st Apr 2022 at 14:00

Last updated: 20th May 2022 at 09:10

Last used: 6th Oct 2022 at 11:05

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Total size: 10.5 KB
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