1035 commits

Author	SHA1	Message	Date
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	fd579ebbb3	Merge branch 'master' into kat_hist	2022-05-11 12:43:11 +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
jasmezz	5d76f1c7ff	Add fasta/gff input option	2022-05-11 12:06:02 +02:00
Jasmin F	9cce4a00b2	Merge branch 'nf-core:master' into antismashlite	2022-05-11 12:03:30 +02:00
Mahesh Binzer-Panchal	0774704038	Merge branch 'master' into genomescope2	2022-05-11 11:38:36 +02:00
Mahesh Binzer-Panchal	cd32c7f744	Merge branch 'master' into kat_hist	2022-05-10 17:03:00 +02:00
Mahesh Binzer-Panchal	b875cfb744	Merge branch 'master' into kat_hist	2022-05-10 14:36:18 +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
Nicolas Vannieuwkerke	ef4857ec54	Updated meta.yml	2022-05-10 12:20:01 +02:00
Moritz E. Beber	09bfe3c618	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-10 12:16:57 +02:00
Moritz E. Beber	b1e134fdd7	docs: describe new file input	2022-05-10 12:16:57 +02:00
Moritz E. Beber	f6936e5270	refactor: accept settings as input	2022-05-10 12:16:57 +02:00
Moritz E. Beber	46a9aabfa3	chore: improve license description	2022-05-10 12:16:57 +02:00
Nicolas Vannieuwkerke	f3d5584ab0	Linting	2022-05-10 12:08:23 +02:00
Nicolas Vannieuwkerke	5db26f9f35	Linting	2022-05-10 12:07:11 +02:00
Nicolas Vannieuwkerke	3a064b0a99	Split the output to different channels	2022-05-10 12:05:42 +02:00
Nicolas Vannieuwkerke	e5d091ad4b	Merge branch 'new-module-rtg/vcfeval' of github.com:nvnieuwk/modules into new-module-rtg/vcfeval	2022-05-10 09:35:44 +02:00
Nicolas Vannieuwkerke	c69d5cc23e	Added evaluation-regions and adjusted the output to now contain all output (and not only the summary)	2022-05-10 09:35:42 +02:00
nvnieuwk	95103fbd79	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-10 09:06:34 +02:00
Praveen Raj S	459a2d1759	Merge branch 'master' into master	2022-05-09 22:16:59 +02:00
Mahesh Binzer-Panchal	f65d896f57	create genomescope2 module	2022-05-09 15:09:15 +00:00
Mahesh Binzer-Panchal	705ad7c3a1	Merge branch 'master' into meryl_unionsum	2022-05-09 16:20:01 +02:00
nvnieuwk	aceb5220cf	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-09 16:18:00 +02:00
Mahesh Binzer-Panchal	83a266ea70	Merge branch 'master' into meryl_unionsum	2022-05-09 16:16:08 +02:00
FriederikeHanssen	adc4ff868c	Merge branch 'master' into samtools_convert	2022-05-09 16:15:24 +02:00
Rike	da79396f06	rename aligned to alignment	2022-05-09 16:07:49 +02:00
Rike	5bd456e5e8	rename file_type to output extension	2022-05-09 16:06:22 +02:00
Rike	1de1c2253e	Combine output after code review	2022-05-09 16:04:58 +02:00
Nicolas Vannieuwkerke	bd7e1414a4	Fixed meta.yml	2022-05-09 15:55:48 +02:00
nvnieuwk	4b8bd9ebf9	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-09 15:51:31 +02:00
Nicolas Vannieuwkerke	1b63d03f8e	adjusted the bed variable name	2022-05-09 15:51:19 +02:00
Nicolas Vannieuwkerke	f6262b4a10	fixed some issues	2022-05-09 15:47:07 +02:00
Rike	24d5e7feed	Code review suggestions	2022-05-09 15:42:55 +02:00
Mahesh Binzer-Panchal	8d86988632	Merge branch 'master' into meryl/histogram	2022-05-09 15:39:32 +02:00
Rike	ef5f145342	Generalize Bam2Cram do either conversion	2022-05-09 15:22:54 +02:00
Mahesh Binzer-Panchal	57fee2b3d6	Add description pattern	2022-05-09 12:56:22 +00:00
Annick Renevey	bf91f9dd9b	update arriba module	2022-05-09 14:55:59 +02:00
Mahesh Binzer-Panchal	6621768550	Update pytest outputs	2022-05-09 12:54:31 +00:00