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