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
*.fastq.gz
:file
FastQ file containing reads that did not align to any database (optional)
*.fastq.gz
versions_fastqscreen
${task.process}
:string
The name of the process
fastqscreen
:string
The name of the tool
fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;"
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
fastqscreen
:string
The name of the tool
fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;"
:eval
The expression to obtain the version of the tool
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.
