This workflow is dependent on other CWL workflows, see the git repository for these.

Workflow for Metagenomics from raw reads to annotated bins.

Main Steps

• workflow_quality.cwl:

• FastQC (control)

• fastp (quality trimming)

• bbmap contamination filter

• SPAdes (Assembly)

• QUAST (Assembly quality report)

• BBmap (Read mapping to assembly)

• MetaBat2 (binning)

• CheckM (bin completeness and contamination)

• GTDB-Tk (bin taxonomic classification)