mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
37 lines
1.3 KiB
YAML
37 lines
1.3 KiB
YAML
name: HISAT2
|
|
description: Graph-based alignment of next generation sequencing reads to a population of genomes
|
|
keywords:
|
|
- Alignment
|
|
- Short reads
|
|
- graph FM Index (GFM)
|
|
- RNA-seq
|
|
tools:
|
|
- fastqc:
|
|
description: |
|
|
HISAT2 is a fast and sensitive alignment program for mapping next-generation
|
|
sequencing reads (whole-genome, transcriptome, and exome sequencing data)
|
|
against the general human population (as well as against a single reference genome).
|
|
Based on GCSA (an extension of BWT for a graph) it is designed and implemented as a
|
|
graph FM index (GFM).
|
|
homepage: http://daehwankimlab.github.io/hisat2/
|
|
documentation: https://ccb.jhu.edu/software/hisat2/manual.shtml
|
|
input:
|
|
-
|
|
- sample_id:
|
|
type: string
|
|
description: Sample identifier
|
|
- reads:
|
|
type: file
|
|
description: Input FastQ file, or pair of files
|
|
output:
|
|
-
|
|
- report:
|
|
type: file
|
|
description: mapping statistics report
|
|
pattern: "*hisat2_stats.txt"
|
|
- alignment:
|
|
type: file
|
|
description: alignment file in BAM format
|
|
pattern: "*hisat2.bam"
|
|
authors:
|
|
- "@FelixKrueger"
|