1641 commits

Author	SHA1	Message	Date
sysbiocoder	fe009b738a	modified: tests/config/pytest_modules.yml	2022-05-16 15:20:15 +00:00
Matthias De Smet	af69ea749d	add module: biobambam/bammerge	2022-05-16 14:39:58 +02:00
Veit Schwämmle	74a1c1400e	Merge branch 'master' into maxquant	2022-05-16 13:26:35 +02:00
Jasmin F	982c9183fa	Merge branch 'master' into antismashlite	2022-05-16 11:42:44 +02:00
Jasmin F	adcfae6cd4	Merge branch 'master' into antismashlite	2022-05-16 10:38:01 +02:00
Rike	eb841d4ea0	revert markduplciatespark changes	2022-05-16 10:33:01 +02:00
FriederikeHanssen	8b4d021189	Merge branch 'master' into gatk_426	2022-05-16 09:50:13 +02:00
Matthias De Smet	5a2e303522	add PE sorted test	2022-05-13 19:16:50 +02:00
Taniguti	ac7fe89a78	Merge branch 'master' into haplocheck	2022-05-13 11:24:10 -03:00
Matthias De Smet	04f82d4d34	fix test name	2022-05-13 15:32:14 +02:00
JIANHONG OU	fadb83cf44	Merge branch 'master' into motus_profile	2022-05-13 09:30:20 -04:00
Matthias De Smet	cbc47767f7	add sort option to bowtie2	2022-05-13 15:26:41 +02:00
Nicolas Vannieuwkerke	a72f06dfe8	removed versions checksum	2022-05-13 14:27:59 +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	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
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	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
James A. Fellows Yates	2eebab4f35	Update tests/modules/motus/profile/test.yml	2022-05-12 20:55:54 +01:00
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
Mahesh Binzer-Panchal	308ab8801d	Merge branch 'master' into kat_hist	2022-05-12 16:52:05 +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
Sateesh Peri	c5d3c90524	Merge branch 'master' into rp3-add-snippy	2022-05-12 07:48:33 -04:00
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
Robert A. Petit III	8b6e1aff38	Merge branch 'master' into rp3-add-snippy	2022-05-11 12:28:27 -06:00
Robert A. Petit III	7ced6e20de	make prettier	2022-05-11 18:00:36 +00:00
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
Mahesh Binzer-Panchal	0199d0efd2	Merge branch 'master' into kat_hist	2022-05-11 16:56:29 +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	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	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
Robert A. Petit III	56e94f625e	remove empty file md5	2022-05-10 21:47:11 +00:00
Robert A. Petit III	44e13ae439	add module for snippy	2022-05-10 21:31:43 +00:00
Mahesh Binzer-Panchal	7a16ece747	Change md5sum to contains	2022-05-10 15:13:25 +00:00
Mahesh Binzer-Panchal	cd32c7f744	Merge branch 'master' into kat_hist	2022-05-10 17:03:00 +02:00
Mahesh Binzer-Panchal	9b4923dcd5	Change test files	2022-05-10 15:02:37 +00:00
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	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	7a5d5f5766	Merge branch 'master' into kat_hist	2022-05-09 13:18:18 +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
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
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
Matthias De Smet	26d2231e85	fix linting	2022-05-06 14:16:38 +02:00
Matthias De Smet	3930ba227b	merge snapaligner modes into one	2022-05-06 14:10:44 +02:00
Mahesh Binzer-Panchal	a9f23bb477	Merge branch 'master' into busco	2022-05-06 13:49:01 +02:00
Mahesh Binzer-Panchal	35c5828f43	Add --auto-lineage option and remove single_end ... Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>	2022-05-06 11:48:21 +00:00
Jose Espinosa-Carrasco	035655e35d	Merge branch 'master' into modules/md5sum	2022-05-06 12:34:14 +02:00
Mahesh Binzer-Panchal	c19e7da59d	Apply suggestions from code review ... Remove versions md5sum Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-06 10:55:48 +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
Ramprasad Neethiraj	db56d80060	Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor	2022-05-06 00:10:28 +02:00
Ramprasad Neethiraj	e4e4f8090c	combine multiple pytor	2022-05-05 23:59:12 +02:00
JIANHONG OU	b8efa2ae7c	Merge branch 'master' into motus_profile	2022-05-05 13:41:54 -04:00
JIANHONG OU	fb5c5d310a	update motus module.	2022-05-05 13:38:46 -04:00
Sateesh Peri	faf45edc5e	Merge branch 'master' into busco	2022-05-05 12:48:39 -04:00
Ramprasad Neethiraj	db2acba71b	Merge branch 'master' into feat/update_cnvpytor	2022-05-05 17:31:10 +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
JIANHONG OU	566c11dacc	Merge branch 'master' into motus_downloaddb	2022-05-05 08:28:10 -04:00
Francesco L	97f318eea6	Merge branch 'master' into firstbranch	2022-05-05 14:25:00 +02:00
Carpanzano	a700a9c15e	Merge branch 'firstbranch' of github.com:carpanz/modules into firstbranch	2022-05-05 13:52:45 +02:00
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
jasmezz	24b9c397dd	Apply suggestions from code review + add support for GFF annotations	2022-05-05 13:14:39 +02:00
MaxUlysse	40dd662fd2	update ensemblvep and snpeff modules	2022-05-05 12:57:14 +02:00
James A. Fellows Yates	e60c6f9bfd	Merge branch 'master' into firstbranch	2022-05-05 10:57:27 +02:00
jasmezz	6a7aec8b41	Remove prokka test workflow	2022-05-05 10:22:02 +02:00
Mahesh Binzer-Panchal	58ea709f7f	Merge branch 'master' into busco	2022-05-05 09:34:14 +02:00
ljmesi	888e122f05	Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq	2022-05-05 08:32:48 +02:00
ljmesi	be8ce6de2a	Remove variable md5sum from the tests	2022-05-05 08:32:45 +02:00
James A. Fellows Yates	35b5ba673f	Merge branch 'master' into motus_downloaddb	2022-05-04 20:58:08 +02:00
Lauri Mesilaakso	e757966566	Merge branch 'master' into add_compression_to_bam2fq	2022-05-04 18:41:36 +03:00
Carpanzano	38faf040ec	missing change in ext.args config	2022-05-04 16:54:15 +02:00
Nicolas Vannieuwkerke	3c07602443	Added the version.yml	2022-05-04 16:51:09 +02:00
Carpanzano	e7b92a7616	fixing md5sum changes	2022-05-04 16:43:22 +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	3c66138672	Linting issue + removed the contains lines	2022-05-04 14:49:17 +02:00
Nicolas Vannieuwkerke	5889d6c923	Another possible fix for the pytest issues	2022-05-04 14:46:15 +02:00
Nicolas Vannieuwkerke	583ea13800	Another try to fix the pytest issues	2022-05-04 14:22:55 +02:00
Nicolas Vannieuwkerke	17dbd2bb82	Linting issue fixed	2022-05-04 14:18:56 +02:00
Nicolas Vannieuwkerke	c1393bf999	Possible fix for the pytest errors?	2022-05-04 14:14:01 +02:00
nvnieuwk	c9808cb97f	Merge branch 'master' into new-module-hap.py	2022-05-04 14:01:02 +02:00
Nicolas Vannieuwkerke	37338ecee3	Finished the module	2022-05-04 14:00:02 +02:00
Mahesh Binzer-Panchal	f65abe1e9a	Prettier	2022-05-04 11:54:51 +00:00
Ramprasad Neethiraj	6541e151bc	Merge branch 'master' into feat/update_cnvpytor	2022-05-04 13:54:46 +02:00
Mahesh Binzer-Panchal	73a8df9522	Fix no genes found test and update test.yml	2022-05-04 11:52:42 +00:00
Nicolas Vannieuwkerke	c517ce9b4d	Added the module and some simple testing	2022-05-04 13:42:12 +02:00
Mahesh Binzer-Panchal	8df20218bf	Add more tests and capture summaries ... Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>	2022-05-04 09:22:43 +00:00
Mahesh Binzer-Panchal	3bb0711b06	Merge branch 'master' into busco	2022-05-04 09:15:46 +02:00
Lauri Mesilaakso	530b5ac661	Merge branch 'master' into add_compression_to_bam2fq	2022-05-04 09:53:46 +03:00
Chris Cheshire	79e64cdd1f	Merge branch 'master' into expected_error_fix	2022-05-03 22:21:28 +01:00
jasmezz	fa9f0753de	Apply review suggestions + add stub for prokka test workflow	2022-05-03 17:30:16 +02:00
Lauri Mesilaakso	12f79c2101	Merge branch 'master' into add_compression_to_bam2fq	2022-05-03 17:03:02 +03:00
ljmesi	a39fa4e003	Fix checksum for one file	2022-05-03 15:47:49 +02:00
Mahesh Binzer-Panchal	636abad8f1	Merge branch 'master' into busco	2022-05-03 15:38:25 +02:00
Nicolas Vannieuwkerke	96d4a31cc1	Moved the BED file to the main tuple	2022-05-03 15:31:05 +02:00
Mahesh Binzer-Panchal	5f4781adaa	Merge branch 'master' into busco	2022-05-03 15:27:10 +02:00
Mahesh Binzer-Panchal	57db28386e	Support batch fasta analysis	2022-05-03 13:26:49 +00:00
ljmesi	034352dbbf	Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq	2022-05-03 15:18:12 +02:00
ljmesi	5510ea39fe	Test --no-name to solve inconsistent checksums	2022-05-03 15:18:09 +02:00
Ramprasad Neethiraj	26311aba2a	fix minor errors	2022-05-03 15:04:37 +02:00
Ramprasad Neethiraj	be085c0173	Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor	2022-05-03 14:55:42 +02:00
Ramprasad Neethiraj	19cfb4e951	update meta files	2022-05-03 14:53:56 +02:00
Ramprasad Neethiraj	46e5752b82	update tests	2022-05-03 14:32:45 +02:00
Lauri Mesilaakso	a65e76e3dd	Merge branch 'master' into add_compression_to_bam2fq	2022-05-03 14:30:54 +03:00
Chris Cheshire	6f35537d40	Merge branch 'master' into expected_error_fix	2022-05-03 12:21:51 +01:00
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
Chris Cheshire	40e6bd9dc1	bowtie2|fix tags error	2022-05-03 12:07:04 +01:00
Chris Cheshire	0f1ee7e50d	bowtie2|test fixes	2022-05-03 12:04:51 +01:00
Chris Cheshire	61f68913fe	Merge branch 'master' into expected_error_fix	2022-05-03 11:49:35 +01:00
Chris Cheshire	768073be63	bowtie2|Added support for large indexes	2022-05-03 11:46:19 +01:00
Mahesh Binzer-Panchal	ddbe6e8f40	Merge branch 'master' into busco	2022-05-03 10:48:03 +02:00
Mahesh Binzer-Panchal	9a72548ee1	Update busco module	2022-05-03 08:42:56 +00:00
Lauri Mesilaakso	6367c6a1ad	Merge branch 'master' into add_compression_to_bam2fq	2022-05-03 11:41:25 +03:00
nvnieuwk	f85787b19e	Merge branch 'master' into vardict-java	2022-05-03 10:17:04 +02:00
Lauri Mesilaakso	773e6f8e93	Merge branch 'master' into add_compression_to_bam2fq	2022-05-03 11:13:55 +03:00
ljmesi	59d6e6e1dd	Add updated md5sums	2022-05-03 09:56:50 +02:00
Ramprasad Neethiraj	6f787aea71	Merge branch 'master' into adding_stub_to_modules	2022-05-03 09:43:16 +02:00
Nicolas Vannieuwkerke	9127f92ddd	Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java	2022-05-03 08:29:50 +02:00
Nicolas Vannieuwkerke	9a10e5beb5	Added the missing inputs in meta.yml + correct notation	2022-05-03 08:29:46 +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
Jill V. Hagey, PhD	23cfb5dd42	Update test.yml	2022-05-02 18:38:48 -04:00
Jill V. Hagey, PhD	db9681029c	Update test.yml	2022-05-02 18:27:01 -04:00
Jill V. Hagey, PhD	7b0d6f96fd	Update test.yml	2022-05-02 18:20:54 -04:00
Jill V. Hagey, PhD	e5d7c80bb5	Update test.yml	2022-05-02 18:13:14 -04:00
Moritz E. Beber	16aa3915e3	feat: add module for slimfastq	2022-05-02 23:16:59 +02:00
Carpanzano	d2e1408b0f	updated content for html file in test yml	2022-05-02 18:44:05 +02:00
carpanz	e8b2445878	updated file location in test yml	2022-05-02 18:43:20 +02:00
Carpanzano	1deb789502	synced withName ext.args with process name	2022-05-02 18:39:45 +02:00
Carpanzano	5136ed29c4	removed include and changed process name due to expected folder name before tokenize	2022-05-02 18:38:59 +02:00
Ramprasad Neethiraj	3194729f82	Merge branch 'master' into adding_stub_to_modules	2022-05-02 18:31:55 +02:00
Jill V. Hagey, PhD	99a8711997	Update tests/modules/srst2/srst2/test.yml ... Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>	2022-05-02 12:26:56 -04:00
Carpanzano	32b8f3f612	adding contain for html output in test yml	2022-05-02 18:21:26 +02:00
carpanz	6e83196634	updating test yml after removing kronadb from test	2022-05-02 18:20:36 +02:00
Carpanzano	b0a2d36ec1	removing kronadb module from testing ktimporttaxonomy test - NB: temporarily using test db while testdb is added to test-datasets	2022-05-02 18:16:08 +02:00
Sateesh Peri	c56b371713	Merge branch 'master' into srst2/srst2	2022-05-02 12:13:11 -04:00
jasmezz	a992a0207e	Merge branch 'antismashlite' of github.com:jasmezz/modules into antismashlite	2022-05-02 17:58:52 +02:00
Jasmin F	b8386c42a7	Merge branch 'nf-core:master' into antismashlite	2022-05-02 17:58:19 +02:00
jasmezz	d19e65d2a2	Merge branch 'antismashlite' of github.com:jasmezz/modules into antismashlite	2022-05-02 17:56:23 +02:00
jasmezz	35cc8152b8	Fix missing test input	2022-05-02 17:55:39 +02:00
Simone Carpanzano	3d9c8a6bb1	Merge branch 'master' into firstbranch	2022-05-02 17:43:33 +02:00
Carpanzano	c9ab26ba8e	synced name of report as in test config	2022-05-02 17:41:55 +02:00
Carpanzano	76a0e3ef04	updated config kraken report name	2022-05-02 17:40:50 +02:00
jvhagey	cd45dc1550	linting test.yml	2022-05-02 11:38:39 -04:00
Jasmin F	883b95bed6	Merge branch 'nf-core:master' into antismashlite	2022-05-02 17:31:43 +02:00
jasmezz	4a4de550b8	Simplify/reduce container mount volumes	2022-05-02 17:30:46 +02:00
jvhagey	24dc2d2113	added tests	2022-05-02 11:30:19 -04:00
Carpanzano	1188264fa2	finished test yml file	2022-05-02 17:25:58 +02:00
carpanz	028dc3cb87	updated test yml file	2022-05-02 17:24:55 +02:00
Carpanzano	3cebcbfc0a	remove taxonomy not used in place of db	2022-05-02 17:13:58 +02:00
Carpanzano	2e4c200a26	remove new line between includes	2022-05-02 17:13:20 +02:00
Jasmin F	235944f797	Merge branch 'master' into antismash_db_output	2022-05-02 17:11:51 +02:00
Carpanzano	700d6ab3f1	errore TDOWNLOAD	2022-05-02 16:55:18 +02:00
Carpanzano	80f107515e	update nextflow.config withName	2022-05-02 16:22:22 +02:00
Carpanzano	42310cbce2	updated config to reflect names in test workflow	2022-05-02 16:14:38 +02:00
Carpanzano	38d9d81aaf	update code	2022-05-02 16:10:57 +02:00
Lucpen	50cc136a78	Update tests/modules/gatk4/mutect2/main.nf ... fix spelling mistake Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>	2022-05-02 15:14:05 +02:00
JIANHONG OU	b14f30936e	Merge branch 'nf-core:master' into motus_downloaddb	2022-05-02 08:42:09 -04:00
JIANHONG OU	0f24e4dcff	add input database and intermediate bam file.	2022-05-02 08:37:12 -04:00
Lucpen	dfabf960dc	Merge branch 'master' into adding_stub_to_modules	2022-05-02 14:20:03 +02:00
JIANHONG OU	3f07761da5	remove the output check for the versions.yml.	2022-05-02 08:19:13 -04:00
Lucpen	da82e06354	fix gatk4_mutect2 test	2022-05-02 14:16:07 +02:00
Lucpen	3a4e415fe2	chores adding dummy files for stubs	2022-05-02 13:30:18 +02:00
James A. Fellows Yates	f1c2f624eb	Update tests/modules/diamond/blastx/main.nf ... Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>	2022-05-02 13:17:22 +02:00
Lucpen	de40c1bf54	chore removing file from test	2022-05-02 13:15:01 +02:00
James Fellows Yates	bd3bfe0817	Add warn of default being used	2022-05-02 12:41:24 +02:00
James Fellows Yates	67b074382e	Fix tests	2022-05-02 12:29:00 +02:00
Lucpen	08d5acbeb6	feat added tests for stubs	2022-05-02 11:59:08 +02:00
James Fellows Yates	58e5c6aece	Make variables consistent	2022-05-02 11:55:43 +02:00
James Fellows Yates	6986975bc0	Fix output channels allow BLAST table customisation	2022-05-02 11:39:07 +02:00
Matthias De Smet	bf416f2307	Merge branch 'master' into vardict-java	2022-05-02 10:43:47 +02:00
James Fellows Yates	996385fb0f	Remove MD5sumfor DIAMOND DAA file due to occasioanlly variability	2022-05-02 09:36:34 +02:00
Ramprasad Neethiraj	9a9f3e97de	fix md5sums	2022-05-01 21:51:40 +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
Carpanzano	41fd2d1557	modifiche	2022-04-29 17:52:12 +02:00
Harshil Patel	4df985a065	Merge branch 'master' into tool/bamtools-split	2022-04-29 16:38:59 +01:00
Carpanzano	6bf0a407f6	modifiche nextflow.config	2022-04-29 15:51:27 +02:00
Simone Carpanzano	d9d0eb393b	Update nextflow.config	2022-04-29 15:39:50 +02:00
Carpanzano	20787514d9	modifiche per il test	2022-04-29 15:11:21 +02:00
James A. Fellows Yates	23c42e9b76	Merge branch 'master' into tool/elprep-merge	2022-04-29 15:11:09 +02:00
Thiseas Christos Lamnidis	4317ad85ae	Passing test	2022-04-29 15:07:32 +02:00
Matthias De Smet	7de207f93f	Merge branch 'master' into diamond-update	2022-04-29 15:02:54 +02:00
Matthias De Smet	bdbf629d93	Merge branch 'master' into tool/bamtools-split	2022-04-29 14:33:28 +02:00
Matthias De Smet	edadc9d216	Merge branch 'master' into tool/elprep-merge	2022-04-29 14:32:12 +02:00
Thiseas Christos Lamnidis	bad832c2ea	Add Sexdeterrmine module	2022-04-29 14:28:45 +02:00
Matthias De Smet	3997d28a77	Merge branch 'master' into subwf/bam_qc	2022-04-29 11:39:18 +02:00
James A. Fellows Yates	983d61763d	Merge branch 'master' into diamond-update	2022-04-29 10:28:38 +02:00
James Fellows Yates	7df2fae746	Clean up test data	2022-04-29 10:26:38 +02:00
James Fellows Yates	42564565b9	Update diamond/blastx diamond/blastp to support all possible output formats	2022-04-29 10:26:17 +02:00
Matthias De Smet	b2e4342105	fix args in nextflow.config	2022-04-29 10:21:22 +02:00
Matthias De Smet	bda132191d	fix args in nextflow.config	2022-04-29 10:13:39 +02:00
CMGG ICT Team	0e01d703ea	remove version md5sum from fixmateinformation	2022-04-29 10:12:52 +02:00
Matthias De Smet	e263f267a7	Merge branch 'master' into bump/picard	2022-04-29 09:48:15 +02:00
Matthias De Smet	ec10f98d55	picard CollectWgsMetrics: update to new cli args (#1578) ... * update to new cli args * remove bam index from tuple, not needed by program * bump picard version Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>	2022-04-29 09:32:32 +02:00
Matthias De Smet	b72ec05d69	drop md5sum from versions.yml	2022-04-29 08:19:42 +02:00