Align fastq reads to a fasta reference using bwa-mem3
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/index information e.g. [ id:‘test’ ]
index
bwa-mem3 genome index files
Directory containing bwa-mem3 index *.{0123,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
:boolean
use samtools sort (true) or samtools view (false)
aligned
*.{sam,bam,cram}
Output SAM/BAM/CRAM file containing read alignments
*.{bai,csi,crai}
Index file for the aligned BAM/CRAM file
versions_bwamem3
${task.process}
:string
The name of the process
bwamem3
The name of the tool
bwa-mem3 version | sed -nE '1 s/^([0-9]+(\.[0-9]+)+).*/\1/p'
:eval
The expression to obtain the version of the tool
versions_samtools
samtools
samtools version | sed '1!d;s/.* //'
versions
Short-read aligner derived from bwa-mem2 with correctness fixes, performance improvements, and methylation-aware alignment.
Tools for dealing with SAM, BAM and CRAM files
