Description

Align reads to multiple reference genomes using fastq-screen

Input

name:type
description
pattern

meta:map

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

reads:file

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

database:directory

fastq screen database folder containing config file and index folders

FastQ_Screen_Genomes

Output

name:type
description
pattern

txt

meta:map

Groovy Map containing sample information

*.txt:file

TXT file containing alignment statistics

*.txt

png

meta:map

Groovy Map containing sample information

*.png:file

PNG file with graphical representation of alignments

*.png

html

meta:map

Groovy Map containing sample information

*.html:file

HTML file containing mapping results as a table and graphical representation

*.html

fastq

meta:map

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

*.fastq.gz:file

FastQ file containing reads that did not align to any database (optional)

*.fastq.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

fastqscreen
GPL-3.0-or-later

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.