986 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
Sofia Stamouli	af8fd18d97	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 15:44:35 +01:00
Sofia Stamouli	b0a6bdee5a	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 15:43:45 +01:00
Sofia Stamouli	c6710db7a9	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 15:42:41 +01:00
Sofia Stamouli	d7c4554b18	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 15:42:10 +01:00
Sofia Stamouli	3eb6a29fb0	Merge branch 'nf-core:dev' into update_output	2022-12-20 15:30:19 +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
Sofia Stamouli	7be3cfc450	Review suggestions	2022-12-20 15:00:17 +01:00
Sofia Stamouli	502a4a81cd	Merge branch 'nf-core:dev' into update_usage	2022-12-20 14:11:05 +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	c23eb968f9	Remove TODOs from test configs	2022-12-16 15:20:06 +01:00
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
Sofia Stamouli	644c4ab831	Review suggestions	2022-12-13 12:00:32 +01:00
Sofia Stamouli	3282f5944b	Apply prettier	2022-12-13 11:28:17 +01:00
Sofia Stamouli	c9e4eba62d	Prettier	2022-12-13 11:26:06 +01:00
sofstam	d99706f43d	Move database section and alphabetical order	2022-12-13 11:23:07 +01:00
Sofia Stamouli	f80adee9e2	Review suggestions and prettier	2022-12-13 09:50:05 +01:00
Sofia Stamouli	1eb3da758b	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-13 09:38:09 +01:00
Sofia Stamouli	97e48075c8	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-13 09:37:43 +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
sofstam	4756dc7f0d	Update output.md	2022-12-12 17:14:57 +01:00
sofstam	b1eb477f33	Update output.md	2022-12-12 17:06:05 +01:00
Sofia Stamouli	a99f89af77	Apply review suggestions	2022-12-12 16:30:28 +01:00
James Fellows Yates	e31e7d3172	Update mOTUs to 3.0.3	2022-12-12 15:42:01 +01:00
Sofia Stamouli	bd5cd0a897	Prettier	2022-12-12 13:34:53 +01:00
sofstam	896a39e68d	Apply review suggestions	2022-12-12 13:19:59 +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
sofstam	c9a6320dac	Merge branch 'update_output' of https://github.com/genomic-medicine-sweden/taxprofiler into update_output ... Conflicts: docs/output.md	2022-12-12 09:13:02 +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
sofstam	b35d26744d	Add classifiers	2022-12-09 17:11:48 +01:00