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Author	SHA1	Message	Date
James Fellows Yates	2439aa69d0	Use specific samplesheet for MALT without LR reads due to GHA memory limits	2023-01-24 10:58:03 +01:00
James Fellows Yates	1a148c5d49	Remove double If and format for readability	2023-01-24 10:48:23 +01:00
James A. Fellows Yates	d56e3133f9	Allow databases of all tools to arrive as tar.gz	2023-01-24 10:45:01 +01:00
James Fellows Yates	1c820f21b3	Dont fail on divide by 0 errors on centrifuge	2023-01-20 17:53:55 +01:00
James A. Fellows Yates	d3bad1d720	Merge pull request #214 from nf-core/local-module-template-sync ... Sync local modules with latest template module structure	2023-01-20 14:41:11 +01:00
James Fellows Yates	606ffc0eb1	Remove platform specificity for MALT	2023-01-20 13:40:59 +01:00
James Fellows Yates	cac6f54d2d	[extra] Fix warn related to recently changed parameter	2023-01-20 13:36:17 +01:00
James Fellows Yates	2d64628552	Fix left-over warns from loca modules	2023-01-20 13:33:43 +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	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
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