(Hybrid) Metagenomics workflow
Version 1

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Workflow Type: Common Workflow Language

Work-in-progress

Workflow (hybrid) metagenomic assembly and binning + GEMs

Accepts both Illumina and Long reads (ONT/PacBio)

Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
Workflow LongRead Quality: https://workflowhub.eu/workflows/337
Kraken2 taxonomic classification of FASTQ reads
SPAdes/Flye (Assembly)
QUAST (Assembly quality report)

Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)

Metabat2/MaxBin2/SemiBin
DAS Tool
CheckM
BUSCO
GTDB-Tk

Workflow Genome-scale metabolic models https://workflowhub.eu/workflows/372 (optional)

CarveMe (GEM generation)
MEMOTE (GEM test suite)
SMETANA (Species METabolic interaction ANAlysis)

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

All tool CWL files and other workflows can be found here:
https://gitlab.com/m-unlock/cwl

How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html

SEEK ID: https://workflowhub.eu/workflows/367?version=1

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	File[]
illumina_reverse_reads	Reverse reads	Reverse sequence file path	File[]
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	File[]?
use_reference_mapped_reads	Keep mapped reads	Continue with reads mapped to the given reference	boolean
keep_filtered_reads	Keep filtered reads	Keep filtered reads in the final output	boolean
deduplicate	Deduplicate reads	Remove exact duplicate reads with fastp	boolean?
kraken_database	Kraken2 database	Absolute path with database location of kraken2	Directory[]?
gtdbtk_data	gtdbtk data directory	Directory containing the GTDBTK repository	Directory?
busco_data	BUSCO dataset	Path to the BUSCO dataset download location	Directory?
ont_basecall_model	ONT Basecalling model	Basecalling model used with guppy default r941_min_high. Available: r941_trans, r941_flip213, r941_flip235, r941_min_fast, r941_min_high, r941_prom_fast, r941_prom_high. (required)	string?
pilon_fixlist	Pilon fix list	A comma-separated list of categories of issues to try to fix	string
metagenome	When working with metagenomes	Metagenome option for assemblers	boolean?
run_spades	Use SPAdes	Run with SPAdes assembler	boolean?
run_flye	Use Flye	Run with Flye assembler	boolean?
run_pilon	Use Pilon	Run with Pilon illumina assembly polishing	boolean?
binning	Run binning workflow	Run with contig binning workflow	boolean?
run_GEM	Run GEM workflow	Run the community genomescale metabolic models workflow on bins	boolean?
run_smetana	Run SMETANA	Run SMETANA (Species METabolic interaction ANAlysis)	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 (prov only)	Not used in this workflow. Output destination used for cwl-prov reporting only.	string?

Steps

ID	Name	Description
workflow_quality_illumina	Quality and filtering workflow	Quality assessment of illumina reads with rRNA filtering option
workflow_quality_nanopore	Nanopore quality and filtering workflow	Quality and filtering workflow for nanopore reads
nanopore_kraken2	Kraken2 Nanopore	Taxonomic classification of nanopore FASTQ reads
illumina_kraken2	Kraken2 Illumina	Taxonomic classification of illumina 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
compress_spades	SPAdes compressed	Compress the large Spades assembly output files
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_pilon	Illumina assembly evaluation	Illumina evaluation of pilon polished assembly with metaQUAST
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
workflow_binning	Binning workflow	Binning workflow to create bins
workflow_GEM	GEM workflow	CarveMe community genomescale metabolic models workflow from bins
keep_readfilter_files_to_folder	Read filtering output folder	Preparation of read filtering output files to a specific output folder
readfilter_files_to_folder	Read filtering output folder	Preparation of read filtering output files to a specific output folder
kraken2_files_to_folder	Kraken2 output folder	Preparation of Kraken2 output files to a specific output folder
spades_files_to_folder	SPADES output to folder	Preparation of SPAdes 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 to folder	Preparation of binning output files and folders to a specific output folder
GEM_files_to_folder	GEM workflow output to folder	Preparation of GEM workflow output files and folders to a specific output folder

Outputs

ID	Name	Description	Type
read_filtering_output_keep	Read filtering output	Read filtering stats + filtered reads	Directory?
read_filtering_output	Read filtering output	Read filtering stats + filtered 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?
gem_output	Community GEM output	Community GEM output folder	Directory?