Description

Align reads to a reference genome using bowtie2

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 reference information
e.g. [ id:‘test’, single_end

]

index (file)

Bowtie2 genome index files

*.ebwt

save_unaligned (boolean)

Save reads that do not map to the reference (true) or discard them (false)
(default: false)

sort_bam (boolean)

use samtools sort (true) or samtools view (false)

true or false

Output

Name (Type)
Description
Pattern

aligned (file)

Output BAM/SAM file containing read alignments

*.{bam,sam}

versions (file)

File containing software versions

versions.yml

fastq (file)

Unaligned FastQ files

*.fastq.gz

log (file)

Aligment log

*.log
included in
atacseq callingcards chipseq circrna crisprseq cutandrun hic marsseq taxprofiler viralrecon
authors
Github user joseespinosa Github user drpatelh
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

bowtie2
GPL-3.0-or-later

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

http://bowtie-bio.sourceforge.net/bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/manual 10.1038/nmeth.1923