* Update HISAT2 build module
* Bump preseq version
* Fix tests
* Add meta.yml for preseq to fix linting
* Auto-detect --genomeSAindexNbases for smaller genomes
* Add placeholder to use human data for the tests
* Add CSI output option to samtools/index
* Fix samtools/index tests
* 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>
* Add default output dir for modules that create indices
* Change path for index module test output
* Fix bowtie2/align tests
* Fixing bowtie/align tests
* Fix genomegenerate test
* Fixing README linting
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
This commit provides a minor refactoring with som
Nextflow code style improvments:
- Replaces `.toGiga()` with `.giga`
- Replaces `tag { foo }` with `tag "$foo"`
- Move publishDir before input declarations. Directives should be
before the first input. Tho this is not enforced, it may be in
future versions.
- Replaces input `file` with `path`
- Remove unnecessary parentheses
