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}

fasta:file

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

*.fasta

Output

name:type
description
pattern

fastq

meta:map

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

]

*.fastq.gz:file

Filtered and trimmed FastQ file

*.{fastq.gz}

versions

versions.yml:file

File containing software versions

versions.yml

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
mag
Github user FynnFreyer
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