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:map
Groovy Map containing genome information e.g. [ id:‘sarscov2’ ]
index:file
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:file
Output BAM file containing read alignments
*.{bam}
log
*.out:file
Log file
*.log
fastq
*fastq.gz:file
Unaligned FastQ files
*.fastq.gz
versions
versions.yml:file
File containing software versions
versions.yml
bowtie is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
