937 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
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
Sofia Stamouli	244fe5e30d	Merge branch 'nf-core:dev' into update_output	2023-01-17 14:47:56 +01:00
James A. Fellows Yates	0cda0d2c51	Merge pull request #213 from nf-core/multiqc-update ... Updates MultiQC to 1.14 to add support for all our MQC modules!	2023-01-17 13:37:44 +01:00
James Fellows Yates	92dff9b453	Standardise file names using only underscore	2023-01-17 10:58:30 +01:00
James Fellows Yates	480248bcfd	Deactivate all classifer columns from general stats	2023-01-17 10:33:35 +01:00
nf-core-bot	11400b016c	[automated] Fix linting with Prettier	2023-01-16 14:11:18 +00:00
James Fellows Yates	0947e9b8ca	Fix mOTUs issues	2023-01-16 15:09:30 +01:00
James Fellows Yates	c8f6d713a3	Add tool names to end of prefix files for easier distinguishing in general stats	2023-01-16 14:49:44 +01:00
James A. Fellows Yates	b34a021db7	Specify the difference between classification/profiling	2023-01-16 14:43:46 +01:00
James Fellows Yates	d6fa45b500	update MultiQC and include latest modules	2023-01-16 14:39:52 +01:00
Sofia Stamouli	06575b537d	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-01-16 12:59:23 +01:00
Sofia Stamouli	0e3f9f0b9a	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-01-16 12:59:13 +01:00
sofstam	9f21181972	Add documentation for output docs	2023-01-12 15:47:29 +01:00
Sofia Stamouli	3b6be07623	Merge branch 'nf-core:dev' into update_output	2023-01-11 16:56:18 +01:00
Sofia Stamouli	33bce738f5	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-01-11 16:50:06 +01:00
Sofia Stamouli	a49a907ad1	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-01-11 16:47:44 +01:00
Sofia Stamouli	953f9585c9	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-01-11 16:47:18 +01:00
Sofia Stamouli	719fc3cf5d	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-01-11 16:46:30 +01:00
James A. Fellows Yates	6dcf619518	Merge pull request #209 from nf-core/module-version-bumps ... Update all modules to make templaite compatible	2022-12-23 23:17:17 +01:00
James Fellows Yates	e5c6db96c8	update all modules to make templaite compatible	2022-12-23 17:23:05 +01:00
James Fellows Yates	ab0c62bdc1	Post-release tweaks to usage.md	2022-12-23 16:23:29 +01:00
James A. Fellows Yates	75a95d5ed8	Merge pull request #143 from genomic-medicine-sweden/update_usage ... Update usage.md	2022-12-23 15:14:12 +01:00
James A. Fellows Yates	acba31a8d6	Update taxprofiler.nf	2022-12-23 15:08:01 +01:00
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	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	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	18c15f8a78	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 20:23:38 +01:00
Sofia Stamouli	fb9de1e212	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 20:23:32 +01:00
Sofia Stamouli	8404c28d08	Review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 20:23:26 +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	2e08c873a0	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 17:34:19 +01:00
Sofia Stamouli	0cbd0a8013	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 17:33:35 +01:00
Sofia Stamouli	af7468522a	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 17:33:18 +01:00
Sofia Stamouli	964771c5f2	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 17:33:04 +01:00