Workflow for Metagenomics from raw reads to annotated bins.

Steps:

• workflow_quality.cwl:

• FastQC (control)

• fastp (trimming)

• Kraken2 (Taxonomic Read Classification

• SPAdes (Assembly)

• QUAST (Assembly quality report)

• BBmap (Read mapping to assembly)

• samtobam (sam to indexed bam)

• metabatContigDepths (jgisummarizebamcontigdepths)

• MetaBat2 (binning)