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5 commits

Author SHA1 Message Date
Robert A. Petit III
c9256616b9
update tests for new config (#384) 
* update tests for new config

* fix quast, update more

* more updates!

* more tests updated

* fix tests, added tabix gff3.gz

* Delete main.nf

Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-04-01 20:22:06 +01:00
Ravneet Bhuller
c5c59d44a1
PR for sequenzautils/bam2seqz (#395) 
* added files

* edited files

* removed file

* README.md edited

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
 2021-04-01 07:08:27 +02:00
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
Jose Espinosa-Carrasco
17fbdf96cb
Fix some module tests after switching to config data (#386) 
* Adding tar.gz kraken2 db to test data

* Update test path files for untar module

* Update test path files for kraken2/run module

* Update test path files for cat/fastq module
 2021-03-24 18:28:07 +00:00
Harshil Patel
83a500e6b0
Use a config containing all test data for module tests (#365) 
* Re-organise all test data

* Fix ECLint

* Fix ECLint agaaainn

* Now is not the time EClint

* Initial commit for test data config

* Rename test data

* Include test config

* Update indents

* Update test for FastQC via config

* Remove quotes of bottom-level variables

* Use underscores in key names

* Get tests working for fastp

* Remove whitespace at beginning of file
 2021-03-24 13:07:37 +00:00