970 commits

Author	SHA1	Message	Date
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	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
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	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
James A. Fellows Yates	8a83ad0518	Merge branch 'master' into motus_profile	2022-05-09 08:16:16 +02:00
nvnieuwk	6fd9246aef	Update modules/rtgtools/vcfeval/main.nf ... Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>	2022-05-09 08:07:33 +02:00
JIANHONG OU	b2542ee079	remove the mgc in metadata for motus_profile.	2022-05-08 06:21:26 -04:00
Harshil Patel	2676f8eef4	Merge branch 'master' into fix-prefetch	2022-05-06 19:33:44 +01:00
Matthias De Smet	0752b82c9f	Merge branch 'master' into update/snapaligner	2022-05-06 18:57:37 +02:00
Moritz E. Beber	ea41c753c0	fix: remove retry label ... Call gets retried by bash script	2022-05-06 17:28:56 +02:00
Moritz E. Beber	dd1c66783a	refactor: use a template to add retrying	2022-05-06 17:26:41 +02:00
Moritz E. Beber	ed09978222	chore: update build number	2022-05-06 17:26:41 +02:00
Mahesh Binzer-Panchal	67481c6d54	Start Meryl count	2022-05-06 15:04:04 +00:00
Nicolas Vannieuwkerke	eb8688d2b8	Merge branch 'new-module-rtg/vcfeval' of github.com:nvnieuwk/modules into new-module-rtg/vcfeval	2022-05-06 16:21:35 +02:00
Nicolas Vannieuwkerke	e271410017	Removed some whitespaces	2022-05-06 16:21:32 +02:00
nvnieuwk	5153e10840	Merge branch 'master' into new-module-rtg/vcfeval	2022-05-06 16:19:17 +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	3499314b96	Update modules/motus/profile/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:19:47 -04:00
JIANHONG OU	4df57b03bd	Update modules/motus/profile/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:11:58 -04:00
JIANHONG OU	6b2f16a0f4	Update modules/motus/profile/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:11:39 -04:00
JIANHONG OU	baeb2bd1c1	Update modules/motus/profile/main.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:11:29 -04:00
JIANHONG OU	4497eb1734	Update modules/motus/profile/main.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:11:22 -04:00
Matthias De Smet	3930ba227b	merge snapaligner modes into one	2022-05-06 14:10:44 +02:00
Mahesh Binzer-Panchal	9fa6b6c1fc	Update meta.yml	2022-05-06 11:56:43 +00:00
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
Ramprasad Neethiraj	e639b1e455	Merge branch 'master' into feat/update_cnvpytor	2022-05-06 12:03:12 +02:00
Matthias De Smet	bd1b80f36e	fix software definitions	2022-05-06 11:07:05 +02:00
Ramprasad Neethiraj	1ccea5ff4d	remove prefix def in callcnvs	2022-05-06 10:56:58 +02:00
Matthias De Smet	1c7205d683	fixed container definitions	2022-05-06 10:44:51 +02:00
Matthias De Smet	77d825e043	fix copy paste errors	2022-05-06 10:39:13 +02:00
Matthias De Smet	09e729ad41	added sha256sum	2022-05-06 10:28:14 +02:00
Matthias De Smet	853b623969	new module: md5sum	2022-05-06 09:20:40 +02:00
Ramprasad Neethiraj	313d76e005	update svdb version	2022-05-06 00:18:16 +02:00
Ramprasad Neethiraj	af73544010	update meta	2022-05-06 00:13:49 +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	e391c65510	fix the version issue for motus_profile.	2022-05-05 15:35:31 -04:00
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
Ramprasad Neethiraj	c183d7b397	Merge branch 'feat/update_cnvpytor' of github.com:ramprasadn/modules into feat/update_cnvpytor	2022-05-05 17:28:59 +02:00
Ramprasad Neethiraj	ea1f5daf44	polish python script in view	2022-05-05 17:28:49 +02:00
Harshil Patel	1289626cc9	Update modules/busco/main.nf	2022-05-05 16:09:45 +01:00
Mahesh Binzer-Panchal	2542ae1823	Update modules/busco/main.nf ... Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>	2022-05-05 16:33:32 +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	47a95388c2	Remove trailing whitespaces (ECLint check)	2022-05-05 13:17:36 +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
Carpanzano	204dfba2d8	fixing ktupdatetaxonomy/meta.yml as suggested in PR	2022-05-05 10:51:22 +02:00
Mahesh Binzer-Panchal	865ad3447a	Update meta.yml output files	2022-05-05 08:23:54 +00:00
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
James A. Fellows Yates	6393a085c5	Apply suggestions from code review	2022-05-05 08:23:51 +02:00
JIANHONG OU	29ee72c693	update meta.yml and remove the cleanup step.	2022-05-04 15:37:12 -04:00
JIANHONG OU	e9c82a5f48	Update modules/motus/downloaddb/meta.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-04 15:29:06 -04:00
James A. Fellows Yates	35b5ba673f	Merge branch 'master' into motus_downloaddb	2022-05-04 20:58:08 +02:00
James A. Fellows Yates	ec5bada3fc	Update modules/motus/downloaddb/meta.yml	2022-05-04 20:55:16 +02:00
Lauri Mesilaakso	e757966566	Merge branch 'master' into add_compression_to_bam2fq	2022-05-04 18:41:36 +03:00
Carpanzano	a6086f549d	recovered process name	2022-05-04 17:28:24 +02:00
Nicolas Vannieuwkerke	3c07602443	Added the version.yml	2022-05-04 16:51:09 +02:00
Carpanzano	8b1711d8a1	recovering old module name	2022-05-04 16:38:10 +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	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	505ab03803	fixed a description	2022-05-04 14:14:53 +02:00
Nicolas Vannieuwkerke	177a7e49f2	Fixed a linting issue	2022-05-04 14:06:42 +02:00
Nicolas Vannieuwkerke	000b8ee2e0	Merge branch 'new-module-hap.py' of github.com:nvnieuwk/modules into new-module-hap.py	2022-05-04 14:05:23 +02:00
Nicolas Vannieuwkerke	065a5d6a7f	Fixed a linting issue	2022-05-04 14:05:21 +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
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
JIANHONG OU	dc59ad0bf5	fix the version issue.	2022-05-03 12:27:39 -04:00
jasmezz	480c4ced78	Update meta.yml	2022-05-03 17:35:16 +02:00
jasmezz	fa9f0753de	Apply review suggestions + add stub for prokka test workflow	2022-05-03 17:30:16 +02:00
Jill V. Hagey, PhD	f02cd618b8	Update meta.yml	2022-05-03 10:09:19 -04:00
Lauri Mesilaakso	12f79c2101	Merge branch 'master' into add_compression_to_bam2fq	2022-05-03 17:03:02 +03:00
Mahesh Binzer-Panchal	1c54c0b1ae	Apply suggestions from code review ... Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>	2022-05-03 16:02:11 +02:00
Matthieu Muffato	6351ec745e	Update contributor list	2022-05-03 14:56:27 +01:00
Matthieu Muffato	4be754b008	It's a file, not a directory	2022-05-03 14:53:17 +01:00
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