Performs fastq alignment to a fasta reference using BWA
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
reads
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
index
BWA genome index files
Directory containing BWA index *.{amb,ann,bwt,pac,sa}
fasta
Reference genome in FASTA format
*.{fasta,fa}
sort_bam
use samtools sort (true) or samtools view (false)
true or false
bam
Output BAM file containing read alignments
*.{bam}
cram
Output CRAM file containing read alignments
*.{cram}
csi
Optional index file for BAM file
*.{csi}
crai
Optional index file for CRAM file
*.{crai}
versions
File containing software versions
versions.yml
BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.