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4 commits

Author SHA1 Message Date
Harshil Patel
b5f6a1da79
Fix linting failures (#552)
* Modules TLC

* Fix all the tests

* Fix linting failures

* Soft-link build files to bypass lint error

* Update software/rseqc/junctionannotation/main.nf
2021-07-01 19:50:14 +01:00
Kevin Menden
043a7d1e3c
remove deprecated test tags (#440)
* remove deprecated test tags

* fix bowtie, gatk4/applybsqr

* fix gatk4 baserecalibrator

* fixed shovill

* fixed yara/mapper

* fixed kallistobustools/ref paths
2021-04-13 18:03:09 +01:00
Harshil Patel
5e18e36895
Update and check tests are running for all modules (#420)
* Fixes for PR 371

* Fix tags

* Add md5sum

* Add md5sums for stringtie

* Fix tests for modules where subtool = build

* Fix pytest_software name conflicts

* Change _ to / in test.yml tags

* Nope...that didnt work

* Fix sequenzautils/bam2seqz tests
2021-04-09 13:47:05 +01:00
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