Metagenomics workflow
Version 6

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Workflow for Metagenomics from raw reads to annotated bins.

Steps:

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)
SAPP (bin annotation)

SEEK ID: https://workflowhub.eu/workflows/64?version=6

Inputs

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[]?

Steps

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
workflow_sapp	Semantic Annotation Platform with Provenance	Semantic Annotation Platform with Provenance to annotate each bin obtained from 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
sapp_files_to_folder	SAPP output	Preparation of sapp output files to a specific output folder

Outputs

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
sapp_output	SAPP Genomes	Folder containing genomes annotated by SAPP	Directory

Creators and Submitter

Creators

Not specified

Submitter

Jasper Koehorst

Discussion Channel

GitLab Issues

License

CC0 1.0

Activity

Views: 199 Downloads: 14

Created: 15th Oct 2020 at 14:55

Last updated: 24th Nov 2020 at 08:46

Last used: 28th Nov 2020 at 04:17

Metagenomics workflow Version 6