Workflow for Illumina paired read quality control, trimming 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

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