Align reads to a reference genome using bowtie2
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
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 reference information e.g. [ id:‘test’, single_end
index:file
Bowtie2 genome index files
*.ebwt
meta3:map
fasta:file
Bowtie2 genome fasta file
*.fasta
save_unaligned:boolean
Save reads that do not map to the reference (true) or discard them (false) (default: false)
sort_bam:boolean
use samtools sort (true) or samtools view (false)
true or false
sam
meta:file
Output SAM file containing read alignments
*.sam
*.sam:file
bam
Output BAM file containing read alignments
*.bam
*.bam:file
cram
Output CRAM file containing read alignments
*.cram
*.cram:file
csi
Output SAM/BAM index for large inputs
*.csi
*.csi:file
crai
Output CRAM index
*.crai
*.crai:file
log
Alignment log
*.log
*.log:file
fastq
Unaligned FastQ files
*.fastq.gz
*fastq.gz:file
versions
versions.yml:file
File containing software versions
versions.yml
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
