Align reads to a reference genome using bowtie2
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.
meta2
Groovy Map containing reference information e.g. [ id:‘test’, single_end:false ]
index
Bowtie2 genome index files
*.ebwt
meta3
fasta
Reference genome FASTA file
*.{fa,fasta,fna}
fai
Reference genome FASTA index file
*.{fai}
save_unaligned
:boolean
Save reads that do not map to the reference (true) or discard them (false) (default: false)
sort_bam
use samtools sort (true) or samtools view (false)
true or false
sam
Groovy Map containing sample information
*.sam
Output SAM file containing read alignments
bam
*.bam
Output BAM file containing read alignments
cram
*.cram
Output CRAM file containing read alignments
csi
*.csi
Output SAM/BAM index for large inputs
crai
*.crai
Output CRAM index
log
*.log
Alignment log
fastq
*fastq.gz
Unaligned FastQ files
*.fastq.gz
versions_bowtie2
${task.process}
:string
The name of the process
bowtie2
The name of the tool
bowtie2 --version 2>&1 | sed -n 's/.*bowtie2-align-s version //p'
:eval
The expression to obtain the version of bowtie2
versions_samtools
samtools
samtools version | sed '1!d;s/.* //'
The expression to obtain the version of samtools
versions_pigz
pigz
pigz --version 2>&1 | sed 's/pigz //'
The expression to obtain the version of pigz
versions
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
