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