nf-core_modules/modules/nextgenmap/meta.yml
Chase Mateusiak 786279b473
New Module: NextGenMap (#1938)
adding nextgenmap module

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
2022-09-27 20:44:47 +01:00

55 lines
1.5 KiB
YAML

name: nextgenmap
description: Performs fastq alignment to a fasta reference using NextGenMap
keywords:
- NextGenMap
- ngm
- alignment
- map
- fastq
- bam
- sam
tools:
- bwa:
description: |
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
homepage: https://github.com/Cibiv/NextGenMap
documentation: https://github.com/Cibiv/NextGenMap/wiki
doi: 10.1093/bioinformatics/btt468
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1, if meta.single_end is true, and 2
if meta.single_end is false.
- fasta:
type: file
description: |
Genomic reference fasta file
pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information. First item of tuple with
bam, below.
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: |
Output BAM file containing read alignments. Second item of tuple with
meta, above
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@cmatkhan"