Create a SNAP index for reference genome
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fasta
:file
Input genome fasta file
altcontigfile
Optional file with a list of alt contig names, one per line.
nonaltcontigfile
Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size.
altliftoverfile
Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit.
index
SNAP genome index files
{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}
snap/*
versions_snapaligner
${task.process}
:string
The name of the process
snap-aligner
The name of the tool
snap-aligner 2>&1 | sed 's/^.*version //;s/.\$//;q'
:eval
The expression to obtain the version of the tool
versions
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
