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