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}
author
Github user FynnFreyer
get in touch
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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
linux.die.net/man/1/zcat

chopper
MIT

A rust command line for filtering and trimming long reads.

args_id: $args2
github.com/wdecoster/chopper 10.1093/bioinformatics/bty149

gzip

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

args_id: $args3
linux.die.net/man/1/gzip