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 information. e.g. [ id:‘test’, single_end:false ]
index{:bash}
BWA genome index files
Directory containing BWA index *.{amb,ann,bwt,pac,sa}
meta3{:bash}
fasta{:bash}
Reference genome in FASTA format
*.{fasta,fa}
sort_bam{:bash}
:boolean
use samtools sort (true) or samtools view (false)
true or false
bam{:bash}
Groovy Map containing sample information
*.bam{:bash}
Output BAM file containing read alignments
*.{bam}
cram{:bash}
*.cram{:bash}
Output CRAM file containing read alignments
*.{cram}
csi{:bash}
*.csi{:bash}
Optional index file for BAM file
*.{csi}
crai{:bash}
*.crai{:bash}
Optional index file for CRAM file
*.{crai}
versions_bwa{:bash}
${task.process}{:bash}
:string
The name of the process
bwa{:bash}
The name of the tool
bwa 2>&1 | sed -n "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{:bash}
BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
