Performs fastq alignment to a reference using NARFMAP
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
NARFMAP hash table
Directory containing NARFMAP hash table *.{cmp,.bin,.txt}
meta3:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
fasta:file
Reference genome in FASTA format
*.{fasta,fa,fna}
sort_bam:boolean
Sort the BAM file after alignment
bam
meta:file
Output BAM file containing read alignments
*.{bam}
*.bam:file
log
*.log:file
Log file of NARFMAP run
*{.log}
versions
versions.yml:file
File containing software versions
versions.yml
narfmap is a fork of the Dragen mapper/aligner Open Source Software.
