Align reads to a reference genome using bowtie
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 genome information e.g. [ id:‘sarscov2’ ]
index{:bash}
Bowtie genome index files
*.ebwt
save_unaligned{:bash}
:boolean
Whether to save fastq files containing the reads which did not align.
bam{:bash}
Groovy Map containing sample information
*.bam{:bash}
Output BAM file containing read alignments
*.{bam}
log{:bash}
*.out{:bash}
Log file
*.log
fastq{:bash}
*fastq.gz{:bash}
Unaligned FastQ files
*.fastq.gz
versions_bowtie{:bash}
${task.process}{:bash}
:string
The name of the process
bowtie{:bash}
The name of the tool
bowtie --version 2>&1 | sed -n 's/.*bowtie-align-s version //p'{:bash}
:eval
The expression to obtain the version of the tool
versions_samtools{:bash}
samtools{:bash}
samtools version | sed '1!d;s/.* //'{:bash}
versions_gzip{:bash}
gzip{:bash}
gzip --version 2>&1 | sed '1!d;s/gzip //'{:bash}
versions{:bash}
bowtie is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
