Performs fastq alignment to a fasta reference using SNAP
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
reads
List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq
*.{fastq.gz,fq.gz,fastq,fq,bam}
meta2
Groovy Map containing reference information e.g. [ id:‘test’, single_end
index
List of SNAP genome index files
{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}
versions
File containing software versions
versions.yml
bam
Aligned BAM file
*.{bam}
bai
Optional aligned BAM file index
*.{bai}
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data