Performs fastq alignment to a fasta reference using BWA-MEME
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
meta2{:bash}
Groovy Map containing reference/index information e.g. [ id:‘test’ ]
index{:bash}
BWA genome index files
Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}
meta3{:bash}
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta{:bash}
Reference genome in FASTA format
*.{fa,fasta,fna}
sort_bam{:bash}
:boolean
use samtools sort (true) or samtools view (false)
true or false
mbuffer{:bash}
:integer
memory for mbuffer in megabytes (default 3072)
samtools_threads{:bash}
number of threads for samtools (default 2)
sam{:bash}
*.sam{:bash}
Output SAM file containing read alignments
*.{sam}
bam{:bash}
*.bam{:bash}
Output BAM file containing read alignments
*.{bam}
cram{:bash}
*.cram{:bash}
Output CRAM file containing read alignments
*.{cram}
crai{:bash}
*.crai{:bash}
Index file for CRAM file
*.{crai}
csi{:bash}
*.csi{:bash}
Index file for BAM file
*.{csi}
versions_bwameme{:bash}
${task.process}{:bash}
:string
The name of the process
bwameme{:bash}
The name of the tool
1.0.6{:bash}
The expression to obtain the version of the tool
versions_samtools{:bash}
Name of the process
samtools{:bash}
Name of the tool
samtools version | sed "1!d;s/.* //"{:bash}
:eval
versions{:bash}
Faster BWA-MEM2 using learned-index
