Performs fastq alignment to a reference using DRAGMAP
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 information e.g. [ id:‘test’, single_end:false ]
hashmap{:bash}
DRAGMAP hash table
Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}
meta3{:bash}
Groovy Map containing reference information e.g. [ id:‘genome’]
fasta{:bash}
Genome fasta reference files
*.{fa,fasta,fna}
sort_bam{:bash}
:boolean
Sort the BAM file
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}
*.{csi}
log{:bash}
*.log{:bash}
Log file
*.{log}
versions_dragmap{:bash}
${task.process}{:bash}
:string
The name of the process
dragmap{:bash}
The name of the tool
dragen-os --version 2>&1{:bash}
:eval
The expression to obtain the version of the tool
versions_samtools{:bash}
samtools{:bash}
samtools version | sed '1!d;s/.* //'{:bash}
versions_pigz{:bash}
pigz{:bash}
pigz --version 2>&1 | sed 's/pigz //'{:bash}
versions{:bash}
Dragmap is the Dragen mapper/aligner Open Source Software.
