712 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
James A. Fellows Yates	e586747680	Add missing comma to list	2022-12-23 15:06:26 +01:00
James A. Fellows Yates	2de049399d	Merge pull request #206 from genomic-medicine-sweden/path_params ... Add path parameters	2022-12-23 15:05:59 +01:00
sofstam	6ebfdcd017	Add path parameters	2022-12-23 13:40:22 +01:00
Sofia Stamouli	59fd676ab3	Merge pull request #205 from genomic-medicine-sweden/optional_untar ... Optional untar on dbs	2022-12-23 13:14:04 +01:00
Sofia Stamouli	41c1ae9d1a	Commit suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-23 12:20:37 +01:00
sofstam	85906ab1cb	Optional untar on dbs	2022-12-23 11:25:57 +01:00
Sofia Stamouli	35b296e5fd	Merge pull request #202 from nf-core/nf-core-template-merge-2.7.2 ... Important! Template update for nf-core/tools v2.7.2	2022-12-21 09:18:40 +01:00
James A. Fellows Yates	361700550e	Merge pull request #203 from nf-core/kraken-uniq-bump ... Bump KrakenUniq version	2022-12-20 21:51:18 +01:00
James A. Fellows Yates	1279437aa1	Apply suggestions from code review	2022-12-20 21:48:08 +01:00
Sofia Stamouli	1706555eff	Prettier	2022-12-20 20:10:05 +01:00
James Fellows Yates	612f532fb2	Bump KrakenUniq version	2022-12-20 20:08:12 +01:00
Sofia Stamouli	24a8da2086	Fix linting	2022-12-20 19:59:55 +01:00
Sofia Stamouli	d691b89727	Merge branch 'dev' into nf-core-template-merge-2.7.2	2022-12-20 15:14:41 +01:00
James A. Fellows Yates	25bb4304e8	Merge pull request #187 from nf-core/revert-pep ... Revert PEP validation back to python samplesheet check	2022-12-20 15:03:18 +01:00
James Fellows Yates	656956b0f9	Black formatting	2022-12-20 14:08:42 +01:00
James Fellows Yates	577da7e835	Remove .first() as the module only executes once anyway and we get a ugly warning	2022-12-20 13:59:14 +01:00
James A. Fellows Yates	41063bc670	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-12-20 13:56:01 +01:00
James Fellows Yates	11db981a88	minor fixes	2022-12-20 13:55:15 +01:00
James A. Fellows Yates	7709245874	Update subworkflows/local/input_check.nf ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-12-20 13:54:05 +01:00
nf-core-bot	ab591e01ff	Template update for nf-core/tools version 2.7.2	2022-12-19 12:10:58 +00:00
Sofia Stamouli	b5c72894fd	Merge pull request #194 from nf-core/multiqc_config ... Configuration of multiqc report	2022-12-16 13:42:55 +01:00
Sofia Stamouli	07a1cfae62	Update assets/multiqc_config.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-16 11:46:42 +01:00
Sofia Stamouli	5a592f086e	Update assets/multiqc_config.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-16 11:46:35 +01:00
Sofia Stamouli	a2c81e33fd	Prettier	2022-12-16 08:38:58 +01:00
Sofia Stamouli	d6db04503e	Configuration of multiqc report	2022-12-15 17:04:45 +01:00
James A. Fellows Yates	aa117e8af9	Merge pull request #192 from nf-core/publishing-fix ... Fix publishing of log files of rpreprocessing steps	2022-12-15 14:39:55 +01:00
James Fellows Yates	0bdc119f9c	Include falco patch	2022-12-15 13:27:41 +01:00
James Fellows Yates	9e6a91aff9	Distinguish Kraken2 from Bracken	2022-12-15 13:25:01 +01:00
James Fellows Yates	3b86a22556	Fix falco publication names	2022-12-15 12:57:49 +01:00
James Fellows Yates	88589fbc53	Fix publishing of log files of rpreprocessing steps	2022-12-15 10:35:06 +01:00
James A. Fellows Yates	578081df2e	Merge pull request #189 from nf-core/database-check ... Adds (native groovy!) database check	2022-12-13 08:43:00 +01:00
James A. Fellows Yates	971f6a6ea8	Merge pull request #190 from nf-core/motus-update-version ... Update mOTUs to 3.0.3	2022-12-12 18:24:05 +01:00
James Fellows Yates	e31e7d3172	Update mOTUs to 3.0.3	2022-12-12 15:42:01 +01:00
James A. Fellows Yates	be85cb408c	Merge pull request #188 from nf-core/bracken-mergetables ... Add Bracken mergetables	2022-12-12 11:26:19 +01:00
James Fellows Yates	7c66968fef	More comments	2022-12-12 11:04:21 +01:00
James Fellows Yates	460f3ca157	Add database sheet validation	2022-12-12 11:03:40 +01:00
James Fellows Yates	3df0a383da	Update combine bracken outputs to include meta for publishing purposes	2022-12-12 10:10:24 +01:00
James Fellows Yates	07bd989bc6	Start work on groovy native datbase checks	2022-12-12 10:02:22 +01:00
James Fellows Yates	4b68e95770	Revert PEP validation back to python samplesheet check	2022-12-12 08:49:13 +01:00
James Fellows Yates	8939ce3e20	Start adding bracken/combinebrackenreports (need smodule update)	2022-12-11 16:52:34 +01:00
James A. Fellows Yates	13c4f44ca6	Merge pull request #185 from nf-core/nf-core-template-merge-2.7.1 ... Important! Template update for nf-core/tools v2.7.1	2022-12-09 12:58:28 +01:00
James Fellows Yates	dca0b86c78	Fix versions	2022-12-09 10:28:48 +01:00
James Fellows Yates	da3d2d96e6	Fix linting	2022-12-09 10:27:50 +01:00
James Fellows Yates	1ccd0a0767	Merge branch 'dev' into nf-core-template-merge-2.7.1	2022-12-09 10:16:17 +01:00
nf-core-bot	36f3b5723b	Template update for nf-core/tools version 2.7.1	2022-12-08 13:18:23 +00:00
James A. Fellows Yates	1687b43596	Merge pull request #183 from nf-core/update-bracken-params ... Update bracken so parameters come directly from database args	2022-12-07 16:39:52 +01:00
James Fellows Yates	d8751787ac	Update bracken so parameters come directly from database args	2022-12-07 07:27:40 +01:00
James Fellows Yates	3dba6405c5	Sets correct default for --shortread_qc_mergepairs	2022-12-06 11:47:16 +01:00
Moritz E. Beber	9064584356	Merge pull request #180 from nf-core/rename-exclude-unmerged ... refactor: change parameter exclude unmerged to include	2022-12-05 10:53:32 +01:00
Moritz E. Beber	24e5bc5410	refactor: use shorter and more explicit syntax	2022-12-04 21:54:10 +01:00