93 commits

Author	SHA1	Message	Date
James A. Fellows Yates	b34a021db7	Specify the difference between classification/profiling	2023-01-16 14:43:46 +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 A. Fellows Yates	4f6eb6fd75	Merge pull request #153 from mjamy/add-krakenuniq-module ... Add krakenuniq module	2022-12-01 09:03:29 +01:00
James Fellows Yates	f414f5dc9c	Add falco to tube map	2022-11-04 18:20:44 +01:00
James Fellows Yates	4275640d9b	update tubemap to include samtools stats	2022-11-04 15:24:15 +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
Moritz E. Beber	bf89525bc2	Merge pull request #146 from nf-core/feat-bracken ... add Bracken to the profiling workflow	2022-10-27 17:35:06 +02:00
Sofia Stamouli	8c3e80b6ea	Add helptest to nextflow_schema,add versions to longread_preprocessing	2022-10-25 11:13:26 +02:00
nf-core-bot	00038db634	[automated] Fix linting with Prettier	2022-10-25 08:51:58 +00:00
Moritz E. Beber	ca7dc308cb	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-10-21 16:36:35 +02:00
Moritz E. Beber	7bd6112133	docs: describe Bracken database usage	2022-10-21 10:18:11 +02:00
Sofia Stamouli	0481bb9449	Prettier	2022-10-18 17:48:40 +02:00
Sofia Stamouli	8eddb32b88	Add Falco as an alternative to FastQC	2022-10-18 17:43:16 +02:00
James A. Fellows Yates	4f27998852	Update usage.md	2022-10-14 14:37:52 +02:00
Sofia Stamouli	e98cd038c7	[skip ci] ... Add description for MALT	2022-10-12 12:56:54 +02:00
Sofia Stamouli	0b16010b92	Add tutorials section	2022-10-12 11:39:03 +02:00
Sofia Stamouli	d09a8e0545	[skip ci]	2022-10-11 17:44:48 +02:00
Sofia Stamouli	17b2ad3199	Add prettier	2022-10-11 17:29:41 +02:00
Sofia Stamouli	f22cf0c921	Update usage.md	2022-10-11 16:41:44 +02:00
Sofia Stamouli	2423c9d87c	Add headers	2022-10-11 15:02:01 +02:00
Moritz E. Beber	fdb8a7f740	Merge branch 'devel' into nf-core-template-merge-2.6	2022-10-05 12:21:54 +02:00
nf-core-bot	51bacb00e6	Template update for nf-core/tools version 2.6	2022-10-05 03:30:53 +00:00
Rafal Stepien	768f9980d8	Add pep_input_base_dir to workflow. Just need to update modules	2022-09-15 12:31:49 -04:00