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