reads_qc

Description¶

Quality control and merging of fastq-format short-reads using fastp, generating fasta

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

Keywords: trimming, quality control, merging, fastq, fasta

This subworkflow uses the following components:

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. e.g. [ id:'test', single_end:false ]	-
`filter_amplicon`	boolean	Specify true to check whether the reads are likely to be AMPLICON or not	-
`ch_reads`	file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.	-
`save_merged`	boolean	Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz`	-

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. `[ id:'test' ]`	-
`seqfu_check`	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`
`suffix_header_check`	file	JSON log file that is empty if no errors were found, or that contains which reads had mismatches if there were errors	`*.json`
`amplicon_check`	env	Optional env variable containing either "AMPLICON", empty otherwise	-
`reads`	file	The trimmed/modified/unmerged fastq reads	`*fastp.fastq.gz`
`reads_se_and_merged`	file	fastp-cleaned single-end reads and merged paired-end reads	`*.merged.fastq.gz`
`fastp_summary_json`	file	fastp results in JSON format	`*.json`
`reads_fasta`	file	FASTA file converted from FASTQ	`*.fasta.gz`
`versions`	file	File containing software versions	`versions.yml`