Description

Filter and trim long read data.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

fastq (file)

FastQ with reads from long read sequencing e.g. PacBio or ONT

*.{fastq.gz}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

fastq (file)

Filtered and trimmed FastQ file

*.{fastq.gz}

Tools

zcat

zcat uncompresses either a list of files on the command line or its standard input and writes the uncompressed data on standard output.

args_id: $args

chopper
MIT

A rust command line for filtering and trimming long reads.

args_id: $args2

gzip

Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77).

args_id: $args3