Workflow Type: Common Workflow Language
Work-in-progress

Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning

  • Workflow Nanopore Quality
  • Kraken2 taxonomic classification of FASTQ reads
  • Flye (de-novo assembly)
  • Medaka (assembly polishing)
  • metaQUAST (assembly quality reports)

When Illumina reads are provided:

All tool CWL files and other workflows can be found here:
Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl
Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows

The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous)
and/or
By using the conda / pip environments as shown in https://git.wur.nl/unlock/docker/-/blob/master/kubernetes/scripts/setup.sh

Inputs

ID Name Description Type
identifier Identifier used Identifier for this dataset used in this workflow
  • string
threads Number of threads Number of threads to use for computational processes
  • int?
memory Maximum memory in MB Maximum memory usage in megabytes
  • int?
nanopore_fastq_files Nanopore reads List of file paths with Nanopore raw reads in fastq format
  • string[]?
illumina_forward_reads illumina forward reads illumina sequenced forward read file
  • string[]?
illumina_reverse_reads illumina reverse reads illumina sequenced reverse file
  • string[]?
use_reference_mapped_reads Use mapped reads Continue with reads mapped to the given reference
  • boolean
deduplicate Deduplicate reads Remove exact duplicate reads (Illumina) with fastp
  • boolean?
kraken_database Kraken2 database Absolute path with database location of kraken2
  • string
basecall_model Basecalling model Basecalling model used with Guppy
  • string
metagenome When working with metagenomes Metagenome option for the flye assembly
  • boolean?
filter_references Contamination reference file(s) Reference fasta file(s) for contamination filtering
  • string[]
pilon_fixlist Pilon fix list A comma-separated list of categories of issues to try to fix
  • string
binning Run binning workflow Run with contig binning workflow
  • boolean?

Steps

ID Name Description
workflow_quality_nanopore Nanopore quality and filtering workflow Quality and filtering workflow for nanopore reads
workflow_quality_illumina Illumina quality and filtering workflow Quality and filtering workflow for illumina reads
nanopore_kraken2 Kraken2 Nanopore Taxonomic classification of Nanopore reads
illumina_kraken2 Kraken2 Illumina Taxonomic classification of FASTQ reads
kraken2_compress Compress kraken2 Compress large kraken2 report file
kraken2_krona Krona Kraken2 Visualization of kraken2 with Krona
flye Nanopore Flye assembly De novo assembly of single-molecule reads with Flye
medaka Medaka polishing of assembly Medaka for polishing of assembled genome
metaquast_medaka assembly evaluation evaluation of polished assembly with metaQUAST
workflow_pilon Pilon worklow Illumina reads assembly polishing with Pilon
metaquast_nanopore_pilon Illumina assembly evaluation Illumina evaluation of pilon polished assembly with metaQUAST
illumina_pilon_readmapping Read mapping Illumina read mapping on pilon assembly for binning
illumina_pilon_sam_to_sorted_bam sam conversion to sorted bam Sam file conversion to a sorted bam file
workflow_binning Binning workflow Binning workflow to create bins
kraken2_files_to_folder Kraken2 output folder Preparation of Kraken2 output files to a specific output folder
flye_files_to_folder Flye output folder Preparation of Flye output files to a specific output folder
metaquast_medaka_files_to_folder Nanopore metaQUAST output folder Preparation of metaQUAST output files to a specific output folder
medaka_files_to_folder Medaka output folder Preparation of Medaka output files to a specific output folder
metaquast_pilon_files_to_folder Illumina metaQUAST output folder Preparation of QUAST output files to a specific output folder
pilon_files_to_folder Pilon output folder Preparation of pilon output files to a specific output folder
assembly_files_to_folder Flye output folder Preparation of Flye output files to a specific output folder
binning_files_to_folder Binning output folder Preparation of quast output files to a specific output folder

Outputs

ID Name Description Type
nanopore_quality_output Read quality and filtering reports Quality reports
  • Directory
illumina_quality_stats Filtered statistics Statistics on quality and preprocessing of the reads
  • Directory
kraken2_output Kraken2 reports Kraken2 taxonomic classification reports
  • Directory
assembly_output Assembly output Output from different assembly steps
  • Directory
binning_output Binning output Binning outputfolders
  • Directory

Version History

Version 3 (latest) Created 20th Apr 2022 at 10:12 by Jasper Koehorst

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Version 2 Created 7th Jan 2022 at 09:32 by Jasper Koehorst

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Frozen Version-2 441b6ec

Version 1 (earliest) Created 6th Jan 2022 at 07:38 by Jasper Koehorst

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Views: 641

Created: 6th Jan 2022 at 07:38

Last updated: 14th Jun 2022 at 10:41

Last used: 28th Jun 2022 at 22:57

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