Workflow Type: Common Workflow Language

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)


ID Name Description Type
identifier identifier used Identifier for this dataset used in this workflow string
forward_reads forward reads forward sequence file locally File[]
reverse_reads reverse reads reverse sequence file locally File[]
threads number of threads number of threads to use for computational processes int?
memory memory usage (mb) maximum memory usage in megabytes int?
pacbio_reads pacbio reads file with PacBio reads locally File[]?
bbmap_reference contamination reference file bbmap reference fasta file for contamination filtering string
run_gtdbtk Run GTDB-Tk Run GTDB-Tk taxonomic bin classification when true boolean


ID Name Description
workflow_quality Quality and filtering workflow Quality assessment of illumina reads with rRNA filtering option
workflow_spades SPADES assembly Genome assembly using spades with illumina/pacbio reads
workflow_quast Quast workflow Genome assembly quality assessment using Quast
workflow_bbmap bbmap read mapping Illumina read mapping using BBmap on assembled contigs
workflow_sam_to_sorted_bam sam conversion to sorted bam Sam file conversion to a sorted indexed bam file
workflow_contig_read_counts samtools idxstats Reports alignment summary statistics
workflow_metabat2_contig_depths contig depths MetabatContigDepths to obtain the depth file used in the MetaBat2 binning process
workflow_metabat2 metabat2 binning Binning procedure using metabat2
workflow_aggregate_bins Depths per bin Depths per bin
workflow_bins_stats Bin assembly stats Table of all bins and there assembly statistics like N50
workflow_getunbinned unbinned_contigs Get unbinned contigs fasta
workflow_bin_readstats Bin and assembly read stats Table general bin and assembly read mapping stats
workflow_checkm CheckM CheckM bin quality assessment
workflow_gtdbtk GTDBTK Taxomic assigment of bins with GTDB-Tk
workflow_compress_gtdbtk Compress GTDB-Tk Compress GTDB-Tk output folder
compress_spades Spades compressed Compress the large Spades assembly output files
spades_files_to_folder SPADES output folder Preparation of spades output files to a specific output folder
quast_files_to_folder QUAST output folder Preparation of quast output files to a specific output folder
sorted_bam_files_to_folder Mapped reads output folder Preparation of mapped reads (sorted bam files) to a specific output folder
metabat_files_to_folder MetaBat2 output folder Preparation of MetaBat2 output files + unbinned contigs to a specific output folder
checkm_files_to_folder CheckM output Preparation of CheckM output files to a specific output folder
gtdbtk_files_to_folder GTBD-Tk output folder Preparation of GTDB-Tk output files to a specific output folder


ID Name Description Type
filtered_stats Filtered statistics Statistics on quality and preprocessing of the reads Directory
spades_output SPADES Metagenome assembly output by SPADES Directory
quast_output QUAST Quast analysis output folder Directory
bam_output BAM files Mapping results in indexed BAM format Directory
metabat2_output MetaBat2 MetaBat2 output directory Directory
checkm_output CheckM CheckM output directory Directory
gtdbtk_output GTDB-Tk GTDB-Tk output directory Directory
help Creators and Submitter
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Views: 1547   Downloads: 64

Created: 15th Oct 2020 at 14:55

Last updated: 19th Oct 2021 at 14:55

Last used: 27th Nov 2021 at 01:57

help Attributions


Version History

Version 11 (latest) Created 18th Oct 2021 at 10:49 by Jasper Koehorst

Added more binning and assembly reports

Version 10 Created 7th Jun 2021 at 18:34 by Jasper Koehorst

No revision comments

Version 9 Created 1st Jun 2021 at 11:43 by Jasper Koehorst

No revision comments

Version 8 Created 6th May 2021 at 07:03 by Jasper Koehorst

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Version 7 Created 8th Jan 2021 at 10:15 by Jasper Koehorst

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