Metagenomics workflow
Version 7


Workflow for Metagenomics from raw reads to annotated bins.


  • 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)


ID Name Description Type
filter_rrna rRNA filtering rRNA read filtering using ... boolean
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?
gzip gzip compression input data is gzip compressed boolean (Optional)
kraken_database Kraken2 database database location of kraken2 string
pacbio_reads pacbio reads file with PacBio reads locally File[]?


ID Name Description
workflow_quality Quality and filtering workflow Quality assessment of illumina reads with rRNA filtering option
workflow_kraken Kraken2 workflow Read classification using the kraken2 database
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
workflow_sam_to_sorted_bam sam conversion to sorted bam sam file conversion to a sorted indexed bam file
workflow_merge_bam_files Merging bam files Merge multiple bam files obtained from the sam to bam conversion module
workflow_metabat_contig_depths depth file from metabat2 Execution of metabat2 to obtain the depth file used in the binning process
workflow_metabat binning process Binning procedure using metabat2
kraken_files_to_folder Kraken output Preparation of kraken output files to a specific output folder
spades_files_to_folder SPADES output Preparation of spades output files to a specific output folder
quast_files_to_folder QUAST output Preparation of quast output files to a specific output folder
sorted_bam_files_to_folder BAM output Preparation of bam files output to a specific output folder
metabat_files_to_folder metabat output Preparation of metabatt output files to a specific output folder


ID Name Description Type
fastqc_output FASTQC Quality reporting by FASTQC Directory[]
filter_output Filtered reads Reads filtered output folder Directory[]
kraken2_output KRAKEN2 Classification output folder by kraken 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
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Views: 472   Downloads: 30

Created: 15th Oct 2020 at 14:55

Last updated: 8th Jan 2021 at 10:15

Last used: 7th Mar 2021 at 21:13

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Version History

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

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