Performs fastq alignment to a fasta reference using NextGenMap
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
reads
:file
List of input FastQ files of size 1, if meta.single_end is true, and 2
if meta.single_end is false.
fasta
:file
Genomic reference fasta file
*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}
Output
name:type
description
pattern
bam
meta
:map
Groovy Map containing sample information. First item of tuple with
bam, below.
e.g. [ id:‘test’, single_end:false ]
*.bam
:file
Output BAM file containing read alignments. Second item of tuple with
meta, above
*.{bam}
versions_nextgenmap
${task.process}
:string
The name of the process
nextgenmap
:string
The name of the tool
ngm --version 2>&1 | sed -n '1s/^.*NextGenMap //p'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
nextgenmap
:string
The name of the tool
ngm --version 2>&1 | sed -n '1s/^.*NextGenMap //p'
:eval
The expression to obtain the version of the tool
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
