105 commits

Author	SHA1	Message	Date
SusiJo	1b93cde9ff	Merge branch 'master' into gatk_spark	2022-06-02 16:24:39 +02:00
nvnieuwk	e107d61069	Update tests/modules/gatk4/haplotypecaller/test.yml ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-02 14:20:15 +02:00
nvnieuwk	e419d306df	Update tests/modules/gatk4/haplotypecaller/test.yml ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-02 14:20:10 +02:00
nvnieuwk	2ce1cf3329	Update tests/modules/gatk4/haplotypecaller/test.yml ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-02 14:20:04 +02:00
nvnieuwk	a6c4276ad7	Update tests/modules/gatk4/haplotypecaller/test.yml ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2022-06-02 14:19:57 +02:00
Nicolas Vannieuwkerke	e53d091a6d	added dragstr model to haplotypecaller	2022-06-02 14:08:09 +02:00
Nicolas Vannieuwkerke	2a45d42868	added the calibratedragstrmodel module	2022-06-02 13:17:06 +02:00
Nicolas Vannieuwkerke	8470f3cb7e	linting	2022-06-01 09:20:20 +02:00
Nicolas Vannieuwkerke	d4f3df4677	Updated the test	2022-06-01 09:17:05 +02:00
nvnieuwk	e4f51d6f59	Merge branch 'master' into new-module-gatk4/ComposeSTRTableFile	2022-06-01 08:59:19 +02:00
Nicolas Vannieuwkerke	1166fb5150	prettier	2022-05-31 16:13:38 +02:00
Nicolas Vannieuwkerke	ec41ea6082	fix test.yml	2022-05-31 16:12:05 +02:00
Nicolas Vannieuwkerke	80366924fd	added gatk4/composestrtablefile	2022-05-31 16:08:13 +02:00
asp8200	98bb45cf4e	Updating test for gatk4/mergevcfs	2022-05-31 13:59:56 +00:00
SusiJo	84f584875e	change string array	2022-05-31 15:50:31 +02:00
SusiJo	58389e550d	test json array	2022-05-31 15:41:50 +02:00
SusiJo	941760f75d	ran prettier	2022-05-31 15:36:02 +02:00
SusiJo	35e296cd7d	added brackets	2022-05-31 15:35:34 +02:00
SusiJo	37b543e3e7	changed to tab	2022-05-31 15:29:27 +02:00
SusiJo	9ef09e6add	adjusted newlines	2022-05-31 14:54:39 +02:00
SusiJo	205576279f	ran prettier again	2022-05-31 14:50:55 +02:00
SusiJo	d484aa1906	adjusted tabs	2022-05-31 14:45:23 +02:00
SusiJo	e083bfafa0	ran prettier	2022-05-31 14:38:45 +02:00
SusiJo	ea526051a4	new test.yml	2022-05-31 14:35:42 +02:00
SusiJo	3117b2973c	added test for metrics	2022-05-31 14:35:29 +02:00
SusiJo	e0e8273f74	adjusted input to use queryname sorted bams	2022-05-31 14:35:18 +02:00
SusiJo	1400f2e683	fixed tests - mixed chr21 + chr22	2022-05-25 16:38:30 +02:00
SusiJo	dd6d838cd7	override userEmulation	2022-05-25 16:37:44 +02:00
Rike	e34dcdd8bc	add brackets to contains	2022-05-23 13:19:42 +02:00
Rike	dc6ad1bff6	add brackets to contains	2022-05-23 13:07:08 +02:00
Rike	093e3aafdd	contains	2022-05-23 13:04:49 +02:00
Rike	a8de9fd085	test path update	2022-05-23 12:53:36 +02:00
Rike	3af61cfbbc	fix input cardinality for index	2022-05-23 12:26:12 +02:00
Rike	a8dac59c50	md5sum not consistent	2022-05-23 12:10:50 +02:00
Rike	2f36a44f61	nf-core create-test-yml	2022-05-23 12:00:31 +02:00
Rike	cd60b4c6eb	add in testdata paths	2022-05-22 13:35:35 +02:00
Rike	bb3e64647b	Merge remote-tracking branch 'origin/master' into gatk_filter	2022-05-18 15:52:47 +02:00
Rike	e8221cf98e	Merge remote-tracking branch 'origin' into gatk_cnnscore	2022-05-18 14:27:25 +02:00
Rike	5ae757121f	Add indices and meta	2022-05-17 23:38:26 +02:00
Rike	15fba1dd7c	add filter variant tranches	2022-05-17 23:01:24 +02:00
Rike	afa0f2a995	update test	2022-05-17 22:53:41 +02:00
Rike	265fd882ca	update test	2022-05-17 19:44:48 +02:00
Rike	5f63904a50	update test	2022-05-17 19:37:18 +02:00
Rike	e0fcbb428d	Add CNNScoreVariants	2022-05-17 19:09:46 +02:00
Rike	eb841d4ea0	revert markduplciatespark changes	2022-05-16 10:33:01 +02:00
FriederikeHanssen	8b4d021189	Merge branch 'master' into gatk_426	2022-05-16 09:50:13 +02:00
Nicolas Vannieuwkerke	a72f06dfe8	removed versions checksum	2022-05-13 14:27:59 +02:00
Nicolas Vannieuwkerke	8a17b6dd0e	added gatk4/splitintervals	2022-05-13 13:46:34 +02:00
Rike	99880654bf	add output default bam	2022-05-12 18:06:15 +02:00
Rike	8792d102ee	fix test input	2022-05-12 17:37:06 +02:00