mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
57 lines
1.5 KiB
YAML
57 lines
1.5 KiB
YAML
name: hisat2_align
|
|
description: Align RNA-Seq reads to a reference with HISAT2
|
|
keywords:
|
|
- align
|
|
- fasta
|
|
- genome
|
|
- reference
|
|
|
|
tools:
|
|
- hisat2:
|
|
description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
|
|
homepage: https://daehwankimlab.github.io/hisat2/
|
|
documentation: https://daehwankimlab.github.io/hisat2/manual/
|
|
doi: "10.1038/s41587-019-0201-4"
|
|
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 and 2 for single-end and paired-end data,
|
|
respectively.
|
|
- index:
|
|
type: file
|
|
description: HISAT2 genome index file
|
|
pattern: "*.ht2"
|
|
- splicesites:
|
|
type: file
|
|
description: Splices sites in gtf file
|
|
pattern: "*.{txt}"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: Output BAM file containing read alignments
|
|
pattern: "*.{bam}"
|
|
- summary:
|
|
type: file
|
|
description: Aligment log
|
|
pattern: "*.log"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@ntoda03"
|