1399 commits

Author	SHA1	Message	Date
James A. Fellows Yates	8dd711aba2	Update tests/modules/motus/profile/main.nf	2022-05-12 20:08:37 +01:00
FriederikeHanssen	868150e1af	Merge branch 'master' into gatk_426	2022-05-12 19:33:07 +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
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	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
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
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
Moritz E. Beber	74b11ccc44	refactor: rename and update subworkflow	2022-05-11 19:24:16 +02:00
Matthias De Smet	dcf9c07fc9	Merge branch 'master' into update/bowtie2-align	2022-05-11 19:08:23 +02:00
Moritz E. Beber	98d8a741ec	tests: add missing paths to config	2022-05-11 18:17:27 +02:00
Moritz E. Beber	888620063b	tests: delete settings for conda	2022-05-11 17:44:49 +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	a83dd33a7e	tests: use remove settings file	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
Harshil Patel	4e603393c3	Merge branch 'master' into update/bowtie2-align	2022-05-11 15:47:37 +01:00
Jasmin F	853e3ec087	Remove commented code ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-05-11 15:56:10 +02:00
Mahesh Binzer-Panchal	fbe2f85e7b	Fix path	2022-05-11 13:53:38 +00:00
Matthias De Smet	94e8c3a882	Update tests/modules/bowtie2/align/test.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:56:03 +02:00
Matthias De Smet	0d00452eca	Update tests/modules/bowtie2/align/test.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:55:45 +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	eae7161a32	tests: add settings input or not and test all branches	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
jasmezz	2b746abfbe	Fix Prettier linting issue	2022-05-11 12:09:52 +02:00
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
Praveen Raj S	237971cd15	Merge branch 'master' into master	2022-05-10 14:35:41 +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
Moritz E. Beber	a303904eb0	chore: add settings file to test data config	2022-05-10 12:19:25 +02:00
Moritz E. Beber	145e2f80e9	tests: run prefetch with and without given settings	2022-05-10 12:16:57 +02:00
Nicolas Vannieuwkerke	3a064b0a99	Split the output to different channels	2022-05-10 12:05:42 +02:00
Nicolas Vannieuwkerke	6008619603	test issue fix?	2022-05-10 10:20:54 +02:00
Nicolas Vannieuwkerke	96c3f895b9	test issue fix?	2022-05-10 10:19:13 +02:00
Nicolas Vannieuwkerke	42fbf80c72	Fixed a test issue with wrong md5sum	2022-05-10 09:57:49 +02:00
Nicolas Vannieuwkerke	f0e8f6ce4d	Linting	2022-05-10 09:36:54 +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
nvnieuwk	4b8bd9ebf9	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-09 15:51:31 +02:00
Mahesh Binzer-Panchal	da93beaf60	Update pytests	2022-05-09 13:50:49 +00:00
Nicolas Vannieuwkerke	f6262b4a10	fixed some issues	2022-05-09 15:47:07 +02:00
Mahesh Binzer-Panchal	8d86988632	Merge branch 'master' into meryl/histogram	2022-05-09 15:39:32 +02:00
nvnieuwk	d6dd4c2e2d	Update tests/modules/rtgtools/vcfeval/test.yml ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-09 15:35:16 +02:00
Rike	ef5f145342	Generalize Bam2Cram do either conversion	2022-05-09 15:22:54 +02:00
Annick Renevey	ac3034696b	update md5sum	2022-05-09 15:19:16 +02:00
Mahesh Binzer-Panchal	0c567f5474	Merge branch 'master' into meryl_unionsum	2022-05-09 15:03:27 +02:00
Mahesh Binzer-Panchal	f0f414d519	Update pytests	2022-05-09 13:00:10 +00:00
Annick Renevey	eed874ace7	update arriba tests	2022-05-09 14:55:59 +02:00
Mahesh Binzer-Panchal	6621768550	Update pytest outputs	2022-05-09 12:54:31 +00:00
Jasmin F	453d5b66a4	Add Bacteroides fragilis GFF file	2022-05-09 14:46:18 +02:00
Mahesh Binzer-Panchal	ce97c87b5d	Merge branch 'master' into meryl_unionsum	2022-05-09 13:51:55 +02:00
Mahesh Binzer-Panchal	a43bc940d6	Add suggestions from code review	2022-05-09 11:15:14 +00:00
Mahesh Binzer-Panchal	129f57ccd9	Add meryl histogram	2022-05-09 08:50:28 +00:00
Mahesh Binzer-Panchal	ad4f8389cb	Add meryl unionsum	2022-05-09 08:33:21 +00:00
Mahesh Binzer-Panchal	32b0fdc9d9	Merge branch 'master' into meryl_count	2022-05-09 10:05:28 +02:00
Mahesh Binzer-Panchal	9ebeb6a702	Update test	2022-05-09 08:05:07 +00:00
Matthias De Smet	3dc18365f6	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-09 10:04:29 +02:00
Mahesh Binzer-Panchal	4591ea2205	atomize	2022-05-09 07:58:58 +00:00
Matthias De Smet	2b91985aa0	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-09 09:43:48 +02:00
Nicolas Vannieuwkerke	d18af7358a	Moved untarring the genome sdf folder to the test itself	2022-05-09 09:20:42 +02:00
Lucpen	bdaed264a7	Merge branch 'master' into correcting_stubs	2022-05-09 08:54:22 +02:00
James A. Fellows Yates	8a83ad0518	Merge branch 'master' into motus_profile	2022-05-09 08:16:16 +02:00
MaxUlysse	3d428e2933	fix spacing	2022-05-07 15:28:40 +02:00
MaxUlysse	1013be2623	fix path to script	2022-05-07 15:22:52 +02:00
Jose Espinosa-Carrasco	e2acf28c8f	Merge branch 'master' into maxulysse-patch-1	2022-05-06 23:53:27 +02:00
Matthias De Smet	0752b82c9f	Merge branch 'master' into update/snapaligner	2022-05-06 18:57:37 +02:00
Matthias De Smet	dd458e3388	fix tags	2022-05-06 18:57:17 +02:00
Maxime U. Garcia	ac217479e9	Update tests/config/test_data.config ... Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>	2022-05-06 18:18:32 +02:00
Maxime U. Garcia	ec7b460fa4	add missing file	2022-05-06 17:54:35 +02:00
Mahesh Binzer-Panchal	67481c6d54	Start Meryl count	2022-05-06 15:04:04 +00:00
nvnieuwk	5153e10840	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-06 16:19:17 +02:00
Nicolas Vannieuwkerke	8c857dee3a	Fixed the sdf folder fetching	2022-05-06 16:16:57 +02:00
Lucpen	8e5fda3b10	Merge branch 'master' into correcting_stubs	2022-05-06 15:37:08 +02:00
Lucpen	971a17a3ab	fix datatest for stubs	2022-05-06 15:34:18 +02:00
Mahesh Binzer-Panchal	7a85760d08	remove 'auto' test	2022-05-06 13:33:27 +00:00
Lucpen	0fa36e6777	fix added correct entry workflow in test.yml	2022-05-06 15:26:34 +02:00
JIANHONG OU	9b50036e9b	add test_bam and -m parameter for motus_profile	2022-05-06 08:56:42 -04:00
JIANHONG OU	c301a406dd	Merge branch 'nf-core:master' into motus_profile	2022-05-06 08:33:43 -04:00
Nicolas Vannieuwkerke	84b354ab6a	Added the rtgtools/vcfeval module	2022-05-06 14:23:40 +02:00
JIANHONG OU	26d5b4da72	Update tests/modules/motus/profile/main.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:19:54 -04:00