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:map
Groovy Map containing reference information. e.g. [ id:‘test’, single_end:false ]
index:file
BWA genome index files
Directory containing BWA index *.{amb,ann,bwt,pac,sa}
meta3:map
fasta:file
Reference genome in FASTA format
*.{fasta,fa}
sort_bam:boolean
use samtools sort (true) or samtools view (false)
true or false
bam
meta:file
Output BAM file containing read alignments
*.{bam}
*.bam:file
cram
Output CRAM file containing read alignments
*.{cram}
*.cram:file
csi
Optional index file for BAM file
*.{csi}
*.csi:file
crai
Optional index file for CRAM file
*.{crai}
*.crai:file
versions
versions.yml:file
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.
