105 commits

Author	SHA1	Message	Date
James A. Fellows Yates	70eb84b8d5	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2023-02-09 08:01:52 +01:00
James Fellows Yates	b3837cce5b	Relax strictness so can supply empty db_params but block if only single parameter with out ;	2023-02-08 15:44:37 +01:00
James Fellows Yates	18886c0cbc	Start trying a different method with maps in profiling	2023-02-07 15:51:25 +01:00
Sofia Stamouli	ffc884b542	Merge branch 'nf-core:dev' into documentation	2023-02-03 15:22:51 +01:00
James A. Fellows Yates	b4f88a29ce	Update docs/usage.md [skip ci]	2023-02-03 09:46:01 +01:00
James A. Fellows Yates	11a8624b39	Add warning about database parameters [skip ci]	2023-02-03 09:42:20 +01:00
sofstam	5363274867	Add some last documentation	2023-02-02 13:58:48 +01:00
sofstam	366745bdbe	Prettier in usage	2023-01-31 09:38:43 +01:00
Sofia Stamouli	5d12785ca4	Merge branch 'nf-core:dev' into update_output	2023-01-25 09:47:30 +01:00
James A. Fellows Yates	9cf2d8763f	[skip ci] Update docs/usage.md ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-01-24 11:50:58 +01:00
James Fellows Yates	085d9e519c	[skip ci] add comment about recommendation to split SR/LR	2023-01-24 11:39:37 +01:00
Sofia Stamouli	7d4035d4c7	Add new line in the description of custom file	2023-01-19 13:44:10 +01:00
James A. Fellows Yates	36629b3dde	Merge branch 'dev' into post-usage-draft-tweaks	2023-01-19 10:36:59 +01:00
James A. Fellows Yates	6e43695264	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-01-19 08:55:23 +01:00
James A. Fellows Yates	6d380fbbff	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-01-19 08:49:55 +01:00
Sofia Stamouli	4dcf8c0b02	Prettier	2023-01-17 15:50:10 +01:00
sofstam	024b683671	Update output and usage	2023-01-17 15:38:56 +01:00
James Fellows Yates	33d4a84237	Add explicit sentnece about classification/profiling	2023-01-17 15:23:59 +01:00
nf-core-bot	11400b016c	[automated] Fix linting with Prettier	2023-01-16 14:11:18 +00:00
James A. Fellows Yates	b34a021db7	Specify the difference between classification/profiling	2023-01-16 14:43:46 +01:00
James Fellows Yates	ab0c62bdc1	Post-release tweaks to usage.md	2022-12-23 16:23:29 +01:00
Sofia Stamouli	ec9c7cfedc	Prettier	2022-12-22 11:10:54 +01:00
Sofia Stamouli	2f291731c1	Merge branch 'nf-core:dev' into update_usage	2022-12-22 11:09:50 +01:00
Sofia Stamouli	1eeb3b337a	Update usage.md	2022-12-22 11:07:09 +01:00
Sofia Stamouli	29978d83b9	Update centrifuge section	2022-12-22 11:03:49 +01:00
Sofia Stamouli	d6e0d404e3	Update docs/usage.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-22 09:18:00 +01:00
Sofia Stamouli	ba43b0daa4	Update docs/usage.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-21 09:26:38 +01:00
Sofia Stamouli	7be3cfc450	Review suggestions	2022-12-20 15:00:17 +01:00
James Fellows Yates	11db981a88	minor fixes	2022-12-20 13:55:15 +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
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
Sofia Stamouli	a99f89af77	Apply review suggestions	2022-12-12 16:30:28 +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 Fellows Yates	4b68e95770	Revert PEP validation back to python samplesheet check	2022-12-12 08:49:13 +01:00
Sofia Stamouli	98f3ab9fd1	Apply prettier	2022-12-09 15:35:51 +01:00
Sofia Stamouli	a622dcaef0	Delete one line	2022-12-09 13:59:37 +01:00
sofstam	5373c58331	Merge branch 'dev' into update_usage	2022-12-09 13:05:42 +01:00
sofstam	97fbc2bceb	Update usage.md	2022-12-09 12:58:51 +01:00
sofstam	3af71d9c63	Merge branch 'dev' into update_usage	2022-12-09 10:35:12 +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
Moritz E. Beber	4529e7e545	refactor: change parameter exclude unmerged to include	2022-12-04 21:36:12 +01:00
James Fellows Yates	de74e4f727	Fix centrifuge warning, filter out long reads from Brakcen, add some caveat docs to usage.md	2022-12-02 12:47:14 +01:00
James Fellows Yates	6459d8920f	Linting!	2022-11-03 14:05:43 +01:00
Mahwash Jamy	aecf308840	Update documentation for krakenuniq	2022-10-31 16:41:35 +00:00