cutadapt

Description¶

Trim adapters and primers from sequencing reads

Keywords: sequencing, primer, trimming, qc, adapter

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

Trim adapters and primers from sequencing reads

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	-
`reads`	file	List of fastq read files	`*.{fastq, fastq.gz}`
`primers`	file	List of at most two primer fasta files The first file should be the forward strand The second file should be the reverse strand If you only want to trim a primer from one strand, then use an empty file as a standin for the second e.g. `[ path/to/fwd_primer, empty.txt ]` for only using the forward primer	`*.fasta`

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	-
`reads`	file	List of trimmed reads files	`*.fastq.gz`
`log`	file	Log file containing stdout from cutadapt	`*.log`
`versions`	file	File containing software versions	`versions.yml`