nf-core_modules/software/hisat2/extractsplicesites/meta.yml
Nicholas Toda e526eae472
Add tests for hisat2 (#366)
* 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>
2021-03-25 21:08:46 +00:00

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YAML

name: hisat2_extractsplicesites
description: Extracts splicing sites from a gtf files
keywords:
- splicing
- gtf
- 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:
- gtf:
type: file
description: Reference gtf annotation file
pattern: "*.{gtf}"
output:
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- splicesites:
type: file
description: Splices sites in gtf file
pattern: "*.{splice_sites.txt}"
authors:
- "@ntoda03"