mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
e526eae472
* initial commit hisat2/build * initial commit hisat2/build * changed names for hisat2 * fixed directory structure and args * added splice site test data * added splice site inputs * replaced list with individual args * fixed removed commas * added test yml file * updated hisat2 conda version * added meta.yml * added meta.yml description * added meta.yml inputs * added meta.yml outputs * update conda version for hisat2 * removed trailing whitespace meta.yml * fixed version number for containers * added test data to test config * updated for new test logic * fix pytest issue? * fix pytest issue * fixed wrong tool in meta.yaml * updated tets.yaml name * handle build bug for testing * handle build bug for testing in yaml * moved test folder to fix build bug * use old hisat2 version to avoid conda giving inconsistent md5sum * initial commit * removed temp file * added meta yaml * add to pytest * added tests * added test yml * add align meta yaml * add hisat2 align to pytest * remove need for splice data by calling process * add hisat2 align se test * add hisat2 align pe test * update names hisat2 align * update software pytest for using mutiple modules * remove splice site test data since using module instead * remove splice site from config since using module instead * fixed extra brace * added hisat2 align test.yml * removed md5sum for bam files * updated build md5sums * Apply suggestions from code review Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> 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"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
|
|
authors:
|
|
- "@ntoda03"
|