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