Description

Align reads to a reference genome using bowtie

Input

name:type
description
pattern

meta:map

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

]

reads:file

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

meta2:map

Groovy Map containing genome information e.g. [ id:‘sarscov2’ ]

index:file

Bowtie genome index files

*.ebwt

save_unaligned:boolean

Whether to save fastq files containing the reads which did not align.

Output

name:type
description
pattern

bam

meta:file

Output BAM file containing read alignments

*.{bam}

*.bam:file

Output BAM file containing read alignments

*.{bam}

log

meta:file

Log file

*.log

*.out:file

Log file

*.log

fastq

meta:file

Unaligned FastQ files

*.fastq.gz

*fastq.gz:file

Unaligned FastQ files

*.fastq.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

bowtie
Artistic-2.0

bowtie is a software package for mapping DNA sequences against a large reference genome, such as the human genome.