Quality assessment, amplicon classification and functional prediction
master @ ba86bfb

Workflow Type: Common Workflow Language

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps:
- FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module for ngtax

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SEEK ID: https://dev.workflowhub.eu/workflows/212?version=1

Inputs

ID	Name	Description	Type
forward_reads	forward reads	forward sequence file locally	File
reverse_reads	reverse reads	reverse sequence file locally	File?
forward_primer	Forward primer	Forward primer used	string
reverse_primer	Reverse primer	Reverse primer used	string?
reference_db	Reference database	Reference database used in FASTA format	string?
rev_read_len	Reverse read length	Read length of the reverse read	int?
for_read_len	Reverse read length	Read length of the reverse read	int
sample	Sample name	Name of the sample being analysed	string
fragment	Subfragment name	Subfragment that is being analysed (e.g. V1-V3 or V5-region)	string
primersRemoved	Primers are removed	Wether the primers are removed or not from the input files	boolean?
threads	number of threads	number of threads to use for computational processes	int?
metadata	Metadata file	UNLOCK assay metadata file	File?

Steps

ID	Name	Description
fastqc	n/a	n/a
reads_to_folder	n/a	n/a
ngtax	n/a	n/a
ngtax_to_tsv-fasta	n/a	n/a
picrust2	n/a	n/a
folder_compression	n/a	n/a
fastqc_files_to_folder	n/a	n/a
ngtax_files_to_folder	n/a	n/a
picrust_files_to_folder	n/a	n/a
phyloseq_files_to_folder	n/a	n/a

Outputs

ID	Name	Description	Type
turtle	n/a	Used for other workflows	File
files_to_folder_fastqc	n/a	n/a	Directory
files_to_folder_ngtax	n/a	n/a	Directory
files_to_folder_picrust2	n/a	n/a	Directory
files_to_folder_phyloseq	n/a	n/a	Directory