Performs fastq alignment to a fasta reference using BWA
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
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/index information e.g. [ id:‘test’ ]
index:file
BWA genome index files
Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}
meta3:map
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta:file
Reference genome in FASTA format
*.{fa,fasta,fna}
sort_bam:boolean
use samtools sort (true) or samtools view (false)
true or false
sam
*.sam:file
Output SAM file containing read alignments
*.{sam}
bam
*.bam:file
Output BAM file containing read alignments
*.{bam}
cram
*.cram:file
Output CRAM file containing read alignments
*.{cram}
crai
*.crai:file
Index file for CRAM file
*.{crai}
csi
*.csi:file
Index file for BAM file
*.{csi}
versions
versions.yml:file
File containing software versions
versions.yml
BWA-mem2 is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
