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Author	SHA1	Message	Date
FriederikeHanssen	8b4d021189	Merge branch 'master' into gatk_426	2022-05-16 09:50:13 +02:00
Jose Espinosa-Carrasco	759223d22d	Merge pull request #1660 from matthdsm/update/bowtie2 ... Bowtie2: add sort option	2022-05-13 20:23:04 +02:00
Matthias De Smet	5a2e303522	add PE sorted test	2022-05-13 19:16:50 +02:00
Matthias De Smet	04f82d4d34	fix test name	2022-05-13 15:32:14 +02:00
Matthias De Smet	cbc47767f7	add sort option to bowtie2	2022-05-13 15:26:41 +02:00
nvnieuwk	919275103a	Merge pull request #1655 from nvnieuwk/new-module-gatk4/splitintervals ... new module: gatk4/splitintervals	2022-05-13 14:43:15 +02:00
Nicolas Vannieuwkerke	6427eeeca0	added tmp-dir + alignment correction	2022-05-13 14:35:22 +02:00
Nicolas Vannieuwkerke	a72f06dfe8	removed versions checksum	2022-05-13 14:27:59 +02:00
Nicolas Vannieuwkerke	1c2a991429	fixed memory warning	2022-05-13 14:25:53 +02:00
Nicolas Vannieuwkerke	d1f824ae66	updated meta.yml	2022-05-13 14:21:48 +02:00
Praveen	e0dccbb5dd	Changed process label to Medium for GATK4/MarkDuplicates	2022-05-13 13:55:14 +02:00
Nicolas Vannieuwkerke	4f6264f7c3	Merge branch 'new-module-gatk4/splitintervals' of github.com:nvnieuwk/modules into new-module-gatk4/splitintervals	2022-05-13 13:48:35 +02:00
Nicolas Vannieuwkerke	9d53577282	linting	2022-05-13 13:48:33 +02:00
nvnieuwk	1d4862ba60	Merge branch 'master' into new-module-gatk4/splitintervals	2022-05-13 13:47:20 +02:00
Nicolas Vannieuwkerke	8a17b6dd0e	added gatk4/splitintervals	2022-05-13 13:46:34 +02:00
Chris Cheshire	af017b32a5	Merge pull request #1653 from luslab/bowtie2-test-fix ... Bowtie2 test fixes	2022-05-13 12:32:28 +01:00
Chris Cheshire	ea55129ba3	Removed version file checksums	2022-05-13 12:20:41 +01:00
Chris Cheshire	9f6a1ae4a4	Merge branch 'master' into bowtie2-test-fix	2022-05-13 12:05:48 +01:00
Chris Cheshire	d816f2bc5d	Reactivated all tests	2022-05-13 12:01:16 +01:00
Mahesh Binzer-Panchal	4acbf9d356	Merge pull request #1641 from mahesh-panchal/genomescope2 ... Genomescope2 module	2022-05-13 11:37:49 +02:00
Mahesh Binzer-Panchal	00826dc2e9	Merge branch 'master' into genomescope2	2022-05-13 11:28:47 +02:00
Mahesh Binzer-Panchal	5df0bcf1be	Update tests/modules/genomescope2/test.yml ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-13 11:27:42 +02:00
Matthias De Smet	fc987d5fcd	Merge pull request #1650 from nvnieuwk/update-module-rtgtools/vcfeval ... Added memory allocation to VCFeval	2022-05-13 10:55:32 +02:00
Nicolas Vannieuwkerke	6fa1c8089a	Added memory allocation to VCFeval	2022-05-13 10:03:20 +02:00
FriederikeHanssen	868150e1af	Merge branch 'master' into gatk_426	2022-05-12 19:33:07 +02:00
Rike	5f7b02189a	reverse again, why did tests pass before	2022-05-12 18:35:51 +02:00
Rike	e3a17b699e	update version	2022-05-12 18:19:33 +02:00
Rike	99880654bf	add output default bam	2022-05-12 18:06:15 +02:00
Rike	3fda3903dc	revert markduplciatespark container	2022-05-12 17:40:42 +02:00
Rike	8792d102ee	fix test input	2022-05-12 17:37:06 +02:00
Rike	a694267b4b	fix empty index input	2022-05-12 17:01:03 +02:00
Rike	b3bd55da76	getpileupsummaries requires intervals files	2022-05-12 16:51:17 +02:00
Rike	f40cfefc08	leftover fixes from refactoring	2022-05-12 16:47:17 +02:00
Rike	15fbf21b28	double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere	2022-05-12 16:16:53 +02:00
Rike	fef5434c4c	Update md5sums	2022-05-12 16:07:12 +02:00
Rike	fd7ee6799a	update version also for spark containers	2022-05-12 15:55:11 +02:00
Rike	169b2b96c1	update gatk version	2022-05-12 15:45:21 +02:00
Jasmin F	85b3c2bcf2	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-12 15:28:19 +02:00
James A. Fellows Yates	3c02e6056c	Merge branch 'master' into antismashlite	2022-05-12 14:53:52 +02:00
Harshil Patel	be0f022053	Merge pull request #1648 from nf-core/refactor-sra-fastq ... refactor: rename and update subworkflow	2022-05-12 11:26:15 +01:00
jasmezz	d2ef476321	Fix Prettier linting error	2022-05-12 12:19:50 +02:00
jasmezz	37cc6f250b	Fixed test.yml	2022-05-12 12:14:19 +02:00
Chris Cheshire	90c67794bf	Added extra tests but error with collection	2022-05-12 10:01:33 +01:00
jasmezz	bd4b70439b	Streamlined some output channels, formatted tests main.nf	2022-05-12 10:56:48 +02:00
Chris Cheshire	4bb0423a1d	Merge remote-tracking branch 'nf-core/master'	2022-05-12 08:57:56 +01:00
Moritz E. Beber	74b11ccc44	refactor: rename and update subworkflow	2022-05-11 19:24:16 +02:00
Matthias De Smet	1dccf12077	Merge pull request #1645 from matthdsm/update/bowtie2-align ... bowtie2: remove code duplication	2022-05-11 19:12:23 +02:00
Matthias De Smet	dcf9c07fc9	Merge branch 'master' into update/bowtie2-align	2022-05-11 19:08:23 +02:00
Harshil Patel	4aaff98c49	Merge pull request #1630 from nf-core/add-ncbi-settings ... feat: add module that verifies NCBI settings	2022-05-11 17:51:24 +01:00
Moritz E. Beber	98d8a741ec	tests: add missing paths to config	2022-05-11 18:17:27 +02:00