77 commits

Author	SHA1	Message	Date
Thomas A. Christensen II	18284e6e32	Add run_krona option to allow skipping Krona chart creation	2022-06-27 08:45:08 -05:00
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 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
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
sofstam	0e5c9e7bdd	Type:boolean for kaiju in nextflow_schema.json	2022-04-14 09:14:05 +02:00
sofstam	6736a2a980	Update README.md, nextflow_schema.json	2022-04-13 19:00:52 +02:00
James Fellows Yates	aa2d07c42a	Fix merge cockup	2022-04-13 14:19:19 +02:00
James A. Fellows Yates	70f94603b0	Merge branch 'dev' into hostremoval	2022-04-13 13:59:51 +02:00
James Fellows Yates	dfeaa0d1fe	Rename subworkflow parameters for consistency	2022-04-13 12:00:28 +02:00
James A. Fellows Yates	967b1f7d6e	Merge branch 'dev' into run-merging	2022-04-12 09:28:10 +02:00
James A. Fellows Yates	025083061e	Merge branch 'dev' into hostremoval	2022-04-11 13:36:03 +02:00
James Fellows Yates	a634814d84	Formatting and fix fastp output	2022-04-08 13:34:00 +02:00
James Fellows Yates	ca011ccc5b	Fix cat_fastq naming logic?	2022-04-08 13:28:37 +02:00
Sofia Stamouli	3d45ac57ae	Prettier	2022-04-07 16:42:22 +02:00
sofstam	26779a4420	Remove db_name from nextflow.config	2022-04-07 16:27:19 +02:00
sofstam	606e5da7d5	Check if PR works with centrifuge/centrifuge module	2022-04-07 16:13:17 +02:00
James A. Fellows Yates	b554aa3e4d	Merge branch 'dev' into hostremoval	2022-04-07 14:00:10 +02:00
Moritz E. Beber	7ab3aa546b	refactor: use flags to publish reads	2022-04-06 10:27:11 +02:00
James Fellows Yates	d46ddd972c	Expand tests and fix schema after review	2022-04-05 11:04:30 +02:00
James Fellows Yates	bb6dd738bd	Merge branch 'complexity-filter-bbduk' of github.com:nf-core/taxprofiler into complexity-filter-bbduk	2022-04-04 21:21:34 +02:00
James Fellows Yates	613f6a5565	Prettier	2022-04-04 21:21:29 +02:00
James A. Fellows Yates	3d662d2e06	Merge branch 'dev' into complexity-filter-bbduk	2022-04-04 21:19:36 +02:00
James Fellows Yates	a384162810	Add prinseq as alternative complexity filtering	2022-04-04 21:16:51 +02:00