Performs fastq alignment to a fasta reference using BWA
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/index information e.g. [ id:‘test’ ]
index{:bash}
BWA genome index files
Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}
meta3{:bash}
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta{:bash}
Reference genome in FASTA format
*.{fa,fasta,fna}
sort_bam{:bash}
:boolean
use samtools sort (true) or samtools view (false)
true or false
sam{:bash}
*.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}
crai{:bash}
*.crai{:bash}
Index file for CRAM file
*.{crai}
csi{:bash}
*.csi{:bash}
Index file for BAM file
*.{csi}
versions_bwamem2{:bash}
${task.process}{:bash}
:string
The name of the process
bwamem2{:bash}
The name of the tool
bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+"{:bash}
:eval
The expression to obtain the version of the tool
versions_samtools{:bash}
samtools{:bash}
samtools version | sed '1!d;s/.* //'{:bash}
versions{:bash}
BWA-mem2 is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
