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:map
Groovy Map containing reference information e.g. [ id:‘test’, single_end:false ]
hashmap:file
DRAGMAP hash table
Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}
meta3:map
Groovy Map containing reference information e.g. [ id:‘genome’]
fasta:file
Genome fasta reference files
*.{fa,fasta,fna}
sort_bam:boolean
Sort the BAM file
sam
*.sam:file
Output SAM file containing read alignments
*.{sam}
bam
meta:file
Output BAM file containing read alignments
*.{bam}
*.bam:file
cram
*.cram:file
Output CRAM file containing read alignments
*.{cram}
crai
*.crai:file
Index file for CRAM file
*.{crai}
csi
*.csi:file
*.{csi}
log
*.log:file
Log file
*.{log}
versions
versions.yml:file
File containing software versions
versions.yml
Dragmap is the Dragen mapper/aligner Open Source Software.
