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