Description

Performs fastq alignment to a fasta reference using SNAP

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

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 (map)

Groovy Map containing reference information
e.g. [ id:‘test’, single_end

]

index (file)

List of SNAP genome index files

{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

bam (file)

Aligned BAM file

*.{bam}

bai (file)

Optional aligned BAM file index

*.{bai}
author
Github user matthdsm
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Tools

snapaligner
Apache v2

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

http://snap.cs.berkeley.edu 1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug https://github.com/amplab/snap 10.1101/2021.11.23.469039