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
Groovy Map containing reference information e.g. [ id:‘test’, single_end:false ]
hashmap
NARFMAP hash table
Directory containing NARFMAP hash table *.{cmp,.bin,.txt}
meta3
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
fasta
Reference genome in FASTA format
*.{fasta,fa,fna}
sort_bam
:boolean
Sort the BAM file after alignment
bam
Output BAM file containing read alignments
*.{bam}
*.bam
log
*.log
Log file of NARFMAP run
*{.log}
versions_narfmap
${task.process}
:string
The name of the process
narfmap
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 //g'
versions
narfmap is a fork of the Dragen mapper/aligner Open Source Software.
