96 commits

Author	SHA1	Message	Date
James Fellows Yates	806208c4b1	Final tweaks to schema, and add a couple of notes for dev guidance on where their various --save_reads parameters are injected	2022-08-31 08:30:26 +02:00
James Fellows Yates	acd0570b4a	Finalise first pass of nextflow json documentation	2022-08-31 07:56:39 +02:00
James Fellows Yates	bdcae4f934	More docs and tweat to usage.md	2022-08-30 16:04:05 +02:00
James Fellows Yates	c2eaa3f6b0	Prettier	2022-08-30 14:33:40 +02:00
James Fellows Yates	d19a473c59	Merge branch 'filtlong-in-tests' into json-schema	2022-08-30 14:33:19 +02:00
James Fellows Yates	8917e29e35	Fix accidental overly zelous search-and-replace	2022-08-30 14:11:48 +02:00
James Fellows Yates	3f8f32cba8	Make longread quality ftilering opt out	2022-08-30 14:08:05 +02:00
James Fellows Yates	2cc07183a0	Standardise QC parameter system and turn on both porechop/filtlong in tests	2022-08-30 13:58:58 +02:00
James Fellows Yates	d4af88e3ff	Make kaiju parameter clearer for documentation purpses and update documentation	2022-08-25 15:50:28 +02:00
James Fellows Yates	d6d51e0e43	Start work on reordering json schema parameters	2022-08-24 15:23:51 +02:00
James Fellows Yates	d8c0e9e7fe	Prettier	2022-07-12 11:41:07 +02:00
James Fellows Yates	a0ee82bf43	Add motus/merge and biom support	2022-07-12 11:39:26 +02:00
James A. Fellows Yates	8082c7d108	Merge pull request #97 from nf-core/malt-to-krona ... Add Krona support for MALT	2022-07-05 15:17:52 +02:00
James A. Fellows Yates	26e31c782d	Merge branch 'dev' into motus	2022-07-04 13:14:42 +02:00
James Fellows Yates	97e6cdf4b4	Add Krona taxonomy DB to schema build	2022-06-30 18:36:13 +02:00
James Fellows Yates	af854f5f34	Update mimetype for database csv as per https://github.com/nf-core/mag/pull/325/files	2022-06-28 12:42:41 +02:00
Thomas A. Christensen II	18284e6e32	Add run_krona option to allow skipping Krona chart creation	2022-06-27 08:45:08 -05:00
JIANHONG OU	c8a59adbce	remove the database auto-download for mOTUs.	2022-06-03 14:13:58 -04:00
James Fellows Yates	3313b90453	Fix JSOn schema	2022-06-03 13:50:48 +02:00
James A. Fellows Yates	96fecb2bfc	Merge branch 'dev' into support-aligned-reads	2022-06-03 13:48:54 +02:00
James A. Fellows Yates	53c4399052	Merge branch 'dev' into motus	2022-06-02 21:38:35 +02:00
James Fellows Yates	2838c136bd	Prettier	2022-06-02 12:51:39 +02:00
James A. Fellows Yates	c9581b1796	Merge branch 'dev' into support-aligned-reads	2022-06-02 12:45:29 +02:00
James Fellows Yates	d3d28da1b1	Update after review	2022-06-02 11:53:53 +02:00
James Fellows Yates	792e2d019b	Fix merge error in schema	2022-05-31 13:06:48 +02:00
James Fellows Yates	310ac6b450	Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong	2022-05-31 13:05:52 +02:00
JIANHONG OU	68d0cc00fa	add motus profile.	2022-05-23 08:05:06 -04:00
James Fellows Yates	0f651873dd	Linting	2022-05-07 06:12:24 +02:00
James Fellows Yates	47a5ae0cff	Add FASTP complexity option	2022-05-07 06:09:05 +02:00
James Fellows Yates	87a1d80519	Add working output for Kraken2/Centrifuge/DIAMOND	2022-05-07 05:22:35 +02:00
ljmesi	6618e8cac6	Change param to a more generic name	2022-05-05 13:20:34 +02:00
ljmesi	557d31dfd2	Add parameter for turning on longread host removal	2022-05-05 13:19:10 +02:00
ljmesi	d94534e8ac	Simplify params which control host removal publish	2022-05-05 09:07:33 +02:00
ljmesi	c833d4fd9a	Fix issues found with prettier	2022-05-03 11:42:05 +02:00
ljmesi	17039ebc6b	Fix type to boolean for flags	2022-05-03 11:07:23 +02:00
ljmesi	fa1c132635	Update nextflow_schema	2022-05-03 11:03:25 +02:00
James Fellows Yates	031cb45934	Add initial longread QC filtering - requires filtlong module update	2022-05-01 07:18:14 +02:00
James Fellows Yates	a4a9b161d8	Lintin	2022-04-29 22:02:44 +02:00
James Fellows Yates	8126d16dee	Add draft version of DIAMOND	2022-04-29 21:59:42 +02:00
Sofia Stamouli	194b89e66a	Prettier	2022-04-26 12:53:39 +02:00
Sofia Stamouli	7afda265c5	Enumerating taxon	2022-04-26 11:27:18 +02:00
Sofia Stamouli	f4480feb9b	Prettier	2022-04-25 17:45:26 +02:00
sofstam	d082d67bcb	Add kaiju2table to taxprofiler	2022-04-25 17:36:29 +02:00
James A. Fellows Yates	cd3c8f6a89	Merge branch 'dev' into hostremoval-publish-fix	2022-04-21 11:43:06 +02:00
Sofia Stamouli	236141f065	Resolve conflicts with dev	2022-04-20 10:17:10 +02:00
James A. Fellows Yates	d16cd75652	Merge branch 'dev' into hostremoval-publish-fix	2022-04-20 09:53:51 +02:00
Sofia Stamouli	4e1b1269be	Apply prettier	2022-04-19 13:11:43 +02:00
James Fellows Yates	b036ed5b73	Prettier	2022-04-17 22:28:18 +02:00
James Fellows Yates	2cfcdf2dd2	Add finer controler over for hostremoval saving	2022-04-17 22:27:04 +02:00
James Fellows Yates	cc73cdd51d	Add generation of taxon-table like output for MALT	2022-04-16 07:42:30 +02:00