849 commits

Author	SHA1	Message	Date
Rike	ba14355891	revert markduplciatespark changes	2022-05-16 09:54:40 +02:00
FriederikeHanssen	8b4d021189	Merge branch 'master' into gatk_426	2022-05-16 09:50:13 +02:00
Matthias De Smet	cbc47767f7	add sort option to bowtie2	2022-05-13 15:26:41 +02:00
Nicolas Vannieuwkerke	6427eeeca0	added tmp-dir + alignment correction	2022-05-13 14:35:22 +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
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	9f6a1ae4a4	Merge branch 'master' into bowtie2-test-fix	2022-05-13 12:05:48 +01:00
Mahesh Binzer-Panchal	00826dc2e9	Merge branch 'master' into genomescope2	2022-05-13 11:28:47 +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	f40cfefc08	leftover fixes from refactoring	2022-05-12 16:47:17 +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
Chris Cheshire	90c67794bf	Added extra tests but error with collection	2022-05-12 10:01:33 +01:00
Matthias De Smet	dcf9c07fc9	Merge branch 'master' into update/bowtie2-align	2022-05-11 19:08:23 +02:00
Moritz E. Beber	b2dbaa9930	refactor: rename module	2022-05-11 17:33:45 +02:00
Moritz E. Beber	23091aabda	refactor: move files to custom section	2022-05-11 17:33:45 +02:00
Moritz E. Beber	e4551a9ab3	refactor: always output settings	2022-05-11 17:33:45 +02:00
Moritz E. Beber	64ff23f3c1	feat: add module that verifies NCBI settings	2022-05-11 17:33:45 +02:00
Matthias De Smet	c8d3de2ad9	restore samtools cmd to defaults	2022-05-11 16:17:30 +02:00
Matthias De Smet	bcd7fe55b1	Update modules/bowtie2/align/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:59:03 +02:00
Matthias De Smet	9097abf277	Update modules/bowtie2/align/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:58:58 +02:00
Matthias De Smet	971a889e2a	Update modules/bowtie2/align/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:57:27 +02:00
Matthias De Smet	b456d8fa0a	Update modules/bowtie2/align/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:57:19 +02:00
Matthias De Smet	ff4b297827	Update modules/bowtie2/align/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:57:11 +02:00
Matthias De Smet	9dd083fa94	Update modules/bowtie2/align/main.nf ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:55:55 +02:00
Matthias De Smet	dcffd93875	Merge branch 'master' into update/bowtie2-align	2022-05-11 13:34:24 +02:00
CMGG ICT Team	3ae8cbfad7	bowtie2: remove code duplication	2022-05-11 13:32:56 +02:00
Moritz E. Beber	0cdf7767a7	refactor: require NCBI user settings always	2022-05-11 13:02:52 +02:00
Moritz E. Beber	d4f13ebfff	refactor: create new settings input	2022-05-11 12:47:54 +02:00
Moritz E. Beber	5d593bdb45	docs: correct license and input description	2022-05-11 12:47:54 +02:00
Mahesh Binzer-Panchal	00fcdd0cba	Merge branch 'master' into genomescope2	2022-05-11 12:42:39 +02:00
Mahesh Binzer-Panchal	d54cf467f4	Update outputs and test data set	2022-05-11 10:42:17 +00:00
Harshil Patel	7be7f404d5	Merge branch 'master' into refactor-prefetch	2022-05-11 11:28:02 +01:00
Mahesh Binzer-Panchal	0774704038	Merge branch 'master' into genomescope2	2022-05-11 11:38:36 +02:00
Praveen Raj S	237971cd15	Merge branch 'master' into master	2022-05-10 14:35:41 +02:00
Nicolas Vannieuwkerke	fa7c947c35	Adjusted meta	2022-05-10 13:33:37 +02:00
Nicolas Vannieuwkerke	b7134855e4	Small update on the output channels	2022-05-10 12:34:52 +02:00
Moritz E. Beber	1b228835e9	refactor: require settings input always	2022-05-10 12:29:42 +02:00
Nicolas Vannieuwkerke	c18391aa49	Updated meta.yml	2022-05-10 12:26:13 +02:00
nvnieuwk	2eb77bd64e	Update modules/rtgtools/vcfeval/main.nf ... Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>	2022-05-10 12:22:56 +02:00
nvnieuwk	29f2d3c284	Update modules/rtgtools/vcfeval/main.nf ... Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>	2022-05-10 12:22:49 +02:00