568 commits

Author	SHA1	Message	Date
Carpanzano	9083d3bb3d	integrating suggestions from PR comments, including recovery of tests for kronadb and more detailed explanation of input database in yml file	2022-05-05 13:51:41 +02:00
Carpanzano	38faf040ec	missing change in ext.args config	2022-05-04 16:54:15 +02:00
Carpanzano	e7b92a7616	fixing md5sum changes	2022-05-04 16:43:22 +02:00
Simone Carpanzano	162f8edf54	Merge branch 'master' into firstbranch	2022-05-04 16:35:25 +02:00
Carpanzano	6b8ca501ed	fixing suggestions from PR	2022-05-04 16:34:52 +02:00
Nicolas Vannieuwkerke	f875aec46b	Split the module into two parts	2022-05-04 15:29:48 +02:00
Nicolas Vannieuwkerke	3c66138672	Linting issue + removed the contains lines	2022-05-04 14:49:17 +02:00
Nicolas Vannieuwkerke	5889d6c923	Another possible fix for the pytest issues	2022-05-04 14:46:15 +02:00
Nicolas Vannieuwkerke	583ea13800	Another try to fix the pytest issues	2022-05-04 14:22:55 +02:00
Nicolas Vannieuwkerke	17dbd2bb82	Linting issue fixed	2022-05-04 14:18:56 +02:00
Nicolas Vannieuwkerke	c1393bf999	Possible fix for the pytest errors?	2022-05-04 14:14:01 +02:00
nvnieuwk	c9808cb97f	Merge branch 'master' into new-module-hap.py	2022-05-04 14:01:02 +02:00
Nicolas Vannieuwkerke	37338ecee3	Finished the module	2022-05-04 14:00:02 +02:00
Nicolas Vannieuwkerke	c517ce9b4d	Added the module and some simple testing	2022-05-04 13:42:12 +02:00
Chris Cheshire	79e64cdd1f	Merge branch 'master' into expected_error_fix	2022-05-03 22:21:28 +01:00
Nicolas Vannieuwkerke	96d4a31cc1	Moved the BED file to the main tuple	2022-05-03 15:31:05 +02:00
Chris Cheshire	6f35537d40	Merge branch 'master' into expected_error_fix	2022-05-03 12:21:51 +01:00
Chris Cheshire	829183ee84	Merge branch 'master' into rp3-add-shigatyper	2022-05-03 12:16:54 +01:00
Chris Cheshire	6015478b72	Merge branch 'master' into add-slimfastq	2022-05-03 12:11:19 +01:00
Chris Cheshire	d7fb969a74	Merge branch 'master' into rp3-add-shigatyper	2022-05-03 12:10:23 +01:00
Chris Cheshire	40e6bd9dc1	bowtie2|fix tags error	2022-05-03 12:07:04 +01:00
Chris Cheshire	0f1ee7e50d	bowtie2|test fixes	2022-05-03 12:04:51 +01:00
Chris Cheshire	61f68913fe	Merge branch 'master' into expected_error_fix	2022-05-03 11:49:35 +01:00
Chris Cheshire	768073be63	bowtie2|Added support for large indexes	2022-05-03 11:46:19 +01:00
nvnieuwk	f85787b19e	Merge branch 'master' into vardict-java	2022-05-03 10:17:04 +02:00
Ramprasad Neethiraj	6f787aea71	Merge branch 'master' into adding_stub_to_modules	2022-05-03 09:43:16 +02:00
Nicolas Vannieuwkerke	9127f92ddd	Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java	2022-05-03 08:29:50 +02:00
Nicolas Vannieuwkerke	9a10e5beb5	Added the missing inputs in meta.yml + correct notation	2022-05-03 08:29:46 +02:00
Matthias De Smet	1687bfcb85	Merge branch 'master' into add-slimfastq	2022-05-03 08:22:49 +02:00
Matthias De Smet	a67c06af81	Merge branch 'master' into vardict-java	2022-05-03 08:22:19 +02:00
Jill V. Hagey, PhD	23cfb5dd42	Update test.yml	2022-05-02 18:38:48 -04:00
Jill V. Hagey, PhD	db9681029c	Update test.yml	2022-05-02 18:27:01 -04:00
Jill V. Hagey, PhD	7b0d6f96fd	Update test.yml	2022-05-02 18:20:54 -04:00
Jill V. Hagey, PhD	e5d7c80bb5	Update test.yml	2022-05-02 18:13:14 -04:00
Moritz E. Beber	16aa3915e3	feat: add module for slimfastq	2022-05-02 23:16:59 +02:00
Carpanzano	d2e1408b0f	updated content for html file in test yml	2022-05-02 18:44:05 +02:00
carpanz	e8b2445878	updated file location in test yml	2022-05-02 18:43:20 +02:00
Carpanzano	1deb789502	synced withName ext.args with process name	2022-05-02 18:39:45 +02:00
Carpanzano	5136ed29c4	removed include and changed process name due to expected folder name before tokenize	2022-05-02 18:38:59 +02:00
Ramprasad Neethiraj	3194729f82	Merge branch 'master' into adding_stub_to_modules	2022-05-02 18:31:55 +02:00
Jill V. Hagey, PhD	99a8711997	Update tests/modules/srst2/srst2/test.yml ... Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>	2022-05-02 12:26:56 -04:00
Carpanzano	32b8f3f612	adding contain for html output in test yml	2022-05-02 18:21:26 +02:00
carpanz	6e83196634	updating test yml after removing kronadb from test	2022-05-02 18:20:36 +02:00
Carpanzano	b0a2d36ec1	removing kronadb module from testing ktimporttaxonomy test - NB: temporarily using test db while testdb is added to test-datasets	2022-05-02 18:16:08 +02:00
Sateesh Peri	c56b371713	Merge branch 'master' into srst2/srst2	2022-05-02 12:13:11 -04:00
Simone Carpanzano	3d9c8a6bb1	Merge branch 'master' into firstbranch	2022-05-02 17:43:33 +02:00
Carpanzano	c9ab26ba8e	synced name of report as in test config	2022-05-02 17:41:55 +02:00
jvhagey	cd45dc1550	linting test.yml	2022-05-02 11:38:39 -04:00
jvhagey	24dc2d2113	added tests	2022-05-02 11:30:19 -04:00
Carpanzano	1188264fa2	finished test yml file	2022-05-02 17:25:58 +02:00