nf-core_modules/modules/snapaligner/index/meta.yml
Matthias De Smet f57f085912
new tool snap-aligner/index (#1506)
* add snapaligner/index

* output fixes

* fix outputs

* fix tests

* update inputs

* fix more bugs

* fix linting

* Update modules/snapaligner/index/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/snapaligner/index/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* fix comments

* fix indents

* fix escaping

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-08 14:41:08 +02:00

39 lines
1.3 KiB
YAML

name: "snapaligner_index"
description: Create a SNAP index for reference genome
keywords:
- index
- fasta
- genome
- reference
tools:
- "snapaligner":
description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data"
homepage: "http://snap.cs.berkeley.edu"
documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
tool_dev_url: "https://github.com/amplab/snap"
doi: "10.1101/2021.11.23.469039"
licence: "['Apache v2']"
input:
- fasta:
type: file
description: Input genome fasta file
- altcontigfile:
type: file
description: Optional file with a list of alt contig names, one per line.
- nonaltcontigfile:
type: file
description: Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size.
- altliftoverfile:
type: file
description: Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit.
output:
- index:
type: file
description: SNAP genome index files
pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@matthdsm"