Performs fastq alignment to a fasta reference using BWA-MEME
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/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
use samtools sort (true) or samtools view (false)
true or false
mbuffer
memory for mbuffer in megabytes (default 3072)
sort_threads
number of threads to used during samtools sort (default 2).
sam
Output SAM file containing read alignments
*.{sam}
bam
Output BAM file containing read alignments
*.{bam}
cram
Output CRAM file containing read alignments
*.{cram}
crai
Index file for CRAM file
*.{crai}
csi
Index file for BAM file
*.{csi}
versions
File containing software versions
versions.yml
Faster BWA-MEM2 using learned-index