seqfu_check

Description

Evaluates the integrity of DNA FASTQ files

Pipelines

This module is used by the following pipelines:

• amplicon-pipeline

Installation

ebi-metagenomics/seqfu/check

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install seqfu/check

Tools

seqfu

DNA sequence utilities for FASTX files

• telatin.github.io/seqfu2/
• 10.3390/bioengineering8050059
• telatin.github.io/seqfu2/tools/check.html
• GPL v3

Input

Name	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	-
fastq	file	Either a single-end FASTQ file, or two paired-end FASTQ files	*.{fastq,fastq.gz,fq,fq.gz}

Output

Name	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	-
tsv	file	TSV file containing output from seqfu/check, first column is either OK or ERR depending on if anything is wrong with the file(s)	*.tsv
versions	file	File containing software versions	versions.yml

People

Authors

@chrisata

Maintainers

@chrisata