(Hybrid) Metagenomics workflow
Version 1

Workflow Type: Common Workflow Language
Work-in-progress

Workflow (hybrid) metagenomic assembly and binning

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
illumina_forward_reads Forward reads Forward sequence file path
  • string[]
illumina_reverse_reads Reverse reads Reverse sequence file path
  • string[]
pacbio_reads PacBio reads File with PacBio reads locally
  • File[]?
nanopore_reads PacBio reads File with PacBio reads locally
  • File[]?
filter_references Contamination reference file bbmap reference fasta file paths for contamination filtering
  • string[]
use_reference_mapped_reads Keep mapped reads Continue with reads mapped to the given reference
  • boolean
deduplicate Deduplicate reads Remove exact duplicate reads with fastp
  • boolean?
kraken_database Kraken2 database Absolute path with database location of kraken2
  • string
binning Run binning workflow Run with contig binning workflow
  • boolean?
run_gtdbtk Run GTDB-Tk Run GTDB-Tk taxonomic bin classification when true
  • boolean
threads Number of threads Number of threads to use for computational processes
  • int?
memory Memory usage (MB) Maximum memory usage in megabytes
  • int?
destination Output Destination Optional Output destination used for cwl-prov reporting.
  • string?

Steps

ID Name Description
workflow_quality Quality and filtering workflow Quality assessment of illumina reads with rRNA filtering option
kraken2 Taxonomic classification with Kraken2 Taxonomic classification of unfiltered FASTQ reads
kraken2_compress Compress kraken2 Compress large kraken2 report file
kraken2_krona Krona Kraken2 Visualization of kraken2 with Krona
spades SPAdes assembly Genome assembly using spades with illumina/pacbio reads
quast Quast workflow Genome assembly quality assessment using Quast
bbmap BBmap read mapping Illumina read mapping using BBmap on assembled contigs
sam_to_sorted_bam sam conversion to sorted bam Sam file conversion to a sorted indexed bam file
contig_read_counts Samtools idxstats Reports alignment summary statistics
compress_spades SPAdes compressed Compress the large Spades assembly output files
workflow_binning Binning workflow Binning workflow to create bins
workflow_GEM GEM workflow CarveME GEM workflow
kraken2_files_to_folder Kraken2 output folder Preparation of Kraken2 output files to a specific output folder
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
binning_files_to_folder Binning output folder Preparation of quast output files to a specific output folder

Outputs

ID Name Description Type
filtered_stats Filtered statistics Statistics on quality and preprocessing of the reads
  • Directory
kraken2_output Kraken2 reports Kraken2 taxonomic classification reports
  • 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?
binning_output Binning output Binning outputfolders
  • Directory?

Version History

Version 1 (earliest) Created 14th Jun 2022 at 09:14 by Bart Nijsse

Initial commit


Open master 62adfb7
help Creators and Submitter
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Views: 387

Created: 14th Jun 2022 at 09:14

Last updated: 14th Jun 2022 at 10:19

Last used: 7th Oct 2022 at 07:08

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Total size: 12.8 KB
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