Performs fastq alignment to a fasta reference using NextGenMap
Input
name:type
description
pattern
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, if meta.single_end is true, and 2
if meta.single_end is false.
fasta{:bash}
:file
Genomic reference fasta file
*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}
Output
name:type
description
pattern
bam{:bash}
meta{:bash}
:map
Groovy Map containing sample information. First item of tuple with
bam, below.
e.g. [ id:‘test’, single_end:false ]
*.bam{:bash}
:file
Output BAM file containing read alignments. Second item of tuple with
meta, above
*.{bam}
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
bwa
MIT
NextGenMap is a flexible highly sensitive short read mapping tool that
handles much higher mismatch rates than comparable algorithms while
still outperforming them in terms of runtime
