Description

Filter and trim long read data.

Input

name:type
description
pattern

meta{:bash}

:map

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

fastq{:bash}

:file

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

*.{fastq.gz}

fasta{:bash}

:file

An optional reference fasta file against which to remove reads that align to it.

*.fasta

Output

name:type
description
pattern

fastq{:bash}

meta{:bash}

:map

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

*.fastq.gz{:bash}

:file

Filtered and trimmed FastQ file

*.{fastq.gz}

versions_chopper{:bash}

${task.process}{:bash}

:string

The name of the process

chopper{:bash}

:string

The name of the tool

chopper --version 2>&1 | cut -d ' ' -f 2{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

chopper{:bash}

:string

The name of the tool

chopper --version 2>&1 | cut -d ' ' -f 2{:bash}

:eval

The expression to obtain the version of the tool

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
included in
mag
maintainer
Github user FynnFreyer
get in touch
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