763 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
James Fellows Yates	606ffc0eb1	Remove platform specificity for MALT	2023-01-20 13:40:59 +01:00
James A. Fellows Yates	d9003924be	Merge pull request #201 from genomic-medicine-sweden/removo_todo ... Remove TODOs from test configs	2023-01-19 13:15:14 +01:00
James A. Fellows Yates	5162240e77	Merge pull request #208 from nf-core/post-usage-draft-tweaks ... Post-release tweaks to usage.md	2023-01-19 11:09:54 +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	49e4e20f84	Merge pull request #212 from nf-core/classification-v-profiling ... Specify the difference between classification/profiling	2023-01-19 10:06:15 +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
James Fellows Yates	33d4a84237	Add explicit sentnece about classification/profiling	2023-01-17 15:23:59 +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
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	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
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