Align reads to multiple reference genomes using fastq-screen
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
database{:bash}
:directory
fastq screen database folder containing config file and index folders
FastQ_Screen_Genomes
Output
name:type
description
pattern
txt{:bash}
meta{:bash}
:map
Groovy Map containing sample information
*.txt{:bash}
:file
TXT file containing alignment statistics
*.txt
png{:bash}
meta{:bash}
:map
Groovy Map containing sample information
*.png{:bash}
:file
PNG file with graphical representation of alignments
*.png
html{:bash}
meta{:bash}
:map
Groovy Map containing sample information
*.html{:bash}
:file
HTML file containing mapping results as a table and graphical representation
*.html
fastq{:bash}
meta{:bash}
:map
Groovy Map containing sample information
*.fastq.gz{:bash}
:file
FastQ file containing reads that did not align to any database (optional)
*.fastq.gz
versions_fastqscreen{:bash}
${task.process}{:bash}
:string
The name of the process
fastqscreen{:bash}
:string
The name of the tool
fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;"{: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
fastqscreen{:bash}
:string
The name of the tool
fastq_screen --version 2>&1 | sed "s/^.*FastQ Screen v//;"{:bash}
: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.
