597 commits

Author	SHA1	Message	Date
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
Taniguti	4728b2bcd2	Merge branch 'master' into haplocheck	2022-05-13 07:49:55 -03:00
Lucas Taniguti	c1ed4e21be	tests: add haplocheck tests	2022-05-13 07:42:34 -03:00
Mahesh Binzer-Panchal	00826dc2e9	Merge branch 'master' into genomescope2	2022-05-13 11:28:47 +02:00
Mahesh Binzer-Panchal	308ab8801d	Merge branch 'master' into kat_hist	2022-05-12 16:52:05 +02:00
James A. Fellows Yates	3c02e6056c	Merge branch 'master' into antismashlite	2022-05-12 14:53:52 +02:00
Robert A. Petit III	8b6e1aff38	Merge branch 'master' into rp3-add-snippy	2022-05-11 12:28:27 -06:00
Moritz E. Beber	b2dbaa9930	refactor: rename module	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
Mahesh Binzer-Panchal	0199d0efd2	Merge branch 'master' into kat_hist	2022-05-11 16:56:29 +02:00
Mahesh Binzer-Panchal	fbe2f85e7b	Fix path	2022-05-11 13:53:38 +00:00
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
Harshil Patel	7be7f404d5	Merge branch 'master' into refactor-prefetch	2022-05-11 11:28:02 +01:00
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
Robert A. Petit III	44e13ae439	add module for snippy	2022-05-10 21:31:43 +00:00
Mahesh Binzer-Panchal	b875cfb744	Merge branch 'master' into kat_hist	2022-05-10 14:36:18 +02:00
Moritz E. Beber	a303904eb0	chore: add settings file to test data config	2022-05-10 12:19:25 +02:00
nvnieuwk	95103fbd79	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-10 09:06:34 +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	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	0c567f5474	Merge branch 'master' into meryl_unionsum	2022-05-09 15:03:27 +02:00
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	7a5d5f5766	Merge branch 'master' into kat_hist	2022-05-09 13:18:18 +02:00
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
Matthias De Smet	2b91985aa0	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-09 09:43:48 +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
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
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
Mahesh Binzer-Panchal	1e55ad987f	Merge branch 'master' into kat_hist	2022-05-06 16:35:51 +02:00
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
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
Matthias De Smet	26d2231e85	fix linting	2022-05-06 14:16:38 +02:00
Mahesh Binzer-Panchal	a9f23bb477	Merge branch 'master' into busco	2022-05-06 13:49:01 +02:00
Matthias De Smet	09e729ad41	added sha256sum	2022-05-06 10:28:14 +02:00
Mahesh Binzer-Panchal	d83281eac9	Merge branch 'master' into kat_hist	2022-05-06 10:02:44 +02:00
Mahesh Binzer-Panchal	9194fb845e	Add module kat hist	2022-05-06 07:54:10 +00:00
Matthias De Smet	853b623969	new module: md5sum	2022-05-06 09:20:40 +02:00
Sateesh Peri	3414d3aba3	Merge branch 'master' into busco	2022-05-05 10:08:55 -04:00
JIANHONG OU	c8f2c44e22	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
JIANHONG OU	a8bc386ea3	Merge branch 'master' into motus_downloaddb	2022-05-05 09:36:25 -04:00
Carpanzano	9083d3bb3d	integrating suggestions from PR comments, including recovery of tests for kronadb and more detailed explanation of input database in yml file	2022-05-05 13:51:41 +02:00
Mahesh Binzer-Panchal	58ea709f7f	Merge branch 'master' into busco	2022-05-05 09:34:14 +02:00
James A. Fellows Yates	35b5ba673f	Merge branch 'master' into motus_downloaddb	2022-05-04 20:58:08 +02:00
Nicolas Vannieuwkerke	3c07602443	Added the version.yml	2022-05-04 16:51:09 +02:00
Simone Carpanzano	162f8edf54	Merge branch 'master' into firstbranch	2022-05-04 16:35:25 +02:00
Carpanzano	6b8ca501ed	fixing suggestions from PR	2022-05-04 16:34:52 +02:00
Nicolas Vannieuwkerke	42bdc5471e	Changed the pytest location of happy	2022-05-04 15:40:34 +02:00
Nicolas Vannieuwkerke	f875aec46b	Split the module into two parts	2022-05-04 15:29:48 +02:00
Mahesh Binzer-Panchal	5986a3efbf	Merge branch 'master' into busco	2022-05-04 15:09:54 +02:00
Nicolas Vannieuwkerke	c517ce9b4d	Added the module and some simple testing	2022-05-04 13:42:12 +02:00
Mahesh Binzer-Panchal	5f4781adaa	Merge branch 'master' into busco	2022-05-03 15:27:10 +02:00
Chris Cheshire	829183ee84	Merge branch 'master' into rp3-add-shigatyper	2022-05-03 12:16:54 +01:00
Chris Cheshire	6015478b72	Merge branch 'master' into add-slimfastq	2022-05-03 12:11:19 +01:00
Chris Cheshire	d7fb969a74	Merge branch 'master' into rp3-add-shigatyper	2022-05-03 12:10:23 +01:00
Mahesh Binzer-Panchal	ddbe6e8f40	Merge branch 'master' into busco	2022-05-03 10:48:03 +02:00
Matthias De Smet	1687bfcb85	Merge branch 'master' into add-slimfastq	2022-05-03 08:22:49 +02:00
Matthias De Smet	a67c06af81	Merge branch 'master' into vardict-java	2022-05-03 08:22:19 +02:00
Moritz E. Beber	16aa3915e3	feat: add module for slimfastq	2022-05-02 23:16:59 +02:00
Sateesh Peri	c56b371713	Merge branch 'master' into srst2/srst2	2022-05-02 12:13:11 -04:00
Simone Carpanzano	3d9c8a6bb1	Merge branch 'master' into firstbranch	2022-05-02 17:43:33 +02:00
Carpanzano	76a0e3ef04	updated config kraken report name	2022-05-02 17:40:50 +02:00
Jasmin F	883b95bed6	Merge branch 'nf-core:master' into antismashlite	2022-05-02 17:31:43 +02:00
JIANHONG OU	b14f30936e	Merge branch 'nf-core:master' into motus_downloaddb	2022-05-02 08:42:09 -04:00
Matthias De Smet	bf416f2307	Merge branch 'master' into vardict-java	2022-05-02 10:43:47 +02:00
James Fellows Yates	44ed38beb8	Merge branch 'diamond-update' of github.com:jfy133/nf-core-modules into diamond-update	2022-04-29 21:06:09 +02:00
James Fellows Yates	39530b5ca7	Bump DIAMOND version to 2.0.15	2022-04-29 21:05:12 +02:00
Simone Carpanzano	05e283405c	Update test_data.config	2022-04-29 00:13:01 +02:00
Simone Carpanzano	a6026e6d30	Update test_data.config	2022-04-29 00:08:27 +02:00
Simone Carpanzano	a76be27d9f	Update test_data.config	2022-04-29 00:06:55 +02:00
Simone Carpanzano	f13a0070d0	Update test_data.config	2022-04-29 00:04:49 +02:00
Simone Carpanzano	10a3718ad6	Update test_data.config ... add 'metagenome' in sarscov2	2022-04-29 00:03:54 +02:00
Matthias De Smet	a7ed1477ee	Merge branch 'master' into tool/elprep-merge	2022-04-28 21:14:30 +02:00
Sateesh Peri	f5c4aecde5	Merge branch 'master' into srst2/srst2	2022-04-28 13:49:51 -04:00
Robert A. Petit III	4b6ee6fc14	Merge branch 'master' into rp3-add-shigatyper	2022-04-28 09:51:36 -06:00
nvnieuwk	c9404ed266	Merge branch 'master' into vardict-java	2022-04-28 14:30:19 +02:00
JIANHONG OU	cdefbec669	add kimporttext module (#1560) ... * add kimporttext module * fix the Prettier error. * fix the Prettier error. * fix the test.yml * fix the test.yml * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update the test files; simplify the main script of krona/ktimporttext. * update the test file url for krona ktimporttext Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-04-28 08:16:26 -04:00
JIANHONG OU	61799e80ab	Merge branch 'nf-core:master' into motus_profile	2022-04-28 08:09:47 -04:00
nvnieuwk	1fd4719e9d	Merge branch 'master' into vardict-java	2022-04-28 09:09:07 +02:00
Jill V. Hagey, PhD	5b6d4fdace	Merge branch 'nf-core:master' into srst2/srst2	2022-04-27 18:19:18 -04:00
jvhagey	839ee59ca1	adding srst2 module	2022-04-27 18:01:28 -04:00
Harshil Patel	1b5d3f5ac2	Bump STAR version to 2.7.10a for RSEM modules (#1573) ... * Bump STAR version to 2.7.10a for RSEM modules * Fix tests	2022-04-27 19:21:26 +01:00
Robert A. Petit III	30bd93602f	Merge branch 'master' into rp3-add-shigatyper	2022-04-27 11:37:13 -06:00