55 commits

Author	SHA1	Message	Date
James Fellows Yates	afba604e8b	Make everything within opt-out, once QC is opted-in	2022-08-30 14:04:34 +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 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	447b8f0905	Get fixed Krona module and add Krona taxonomy to test profile	2022-07-01 17:21:19 +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
James Fellows Yates	9462032d00	Fix MALT save_alignemnts reads and some clean up	2022-06-03 22:29:04 +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 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
JIANHONG OU	4d77b47e8d	create a new test profile config for mOTUs.	2022-05-31 08:47:38 -04:00
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	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
James Fellows Yates	031cb45934	Add initial longread QC filtering - requires filtlong module update	2022-05-01 07:18:14 +02:00
James Fellows Yates	0630fce3b5	Tweak based on official DIAMOND test-data	2022-04-30 08:11:40 +02:00
James Fellows Yates	8126d16dee	Add draft version of DIAMOND	2022-04-29 21:59:42 +02:00
James A. Fellows Yates	d850333e11	Linting	2022-04-20 13:42:26 +02:00
James A. Fellows Yates	d031322c16	Update test.config	2022-04-20 13:41:01 +02:00
sofstam	1b7ff2265d	Update usage.md, reformat test.config and modules.config	2022-04-19 13:04:58 +02:00
sofstam	68ce5843a4	Add kaiju in taxprofiler	2022-04-13 18:51:56 +02:00
James A. Fellows Yates	5e80df0f94	Apply suggestions from code review	2022-04-13 15:27:53 +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	025083061e	Merge branch 'dev' into hostremoval	2022-04-11 13:36:03 +02:00
Sofia Stamouli	48d28cf8d4	Update conf/test.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-04-08 10:00:10 +02:00
Sofia Stamouli	2dfe3b3cc1	Update conf/test.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-04-08 10:00:04 +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
James Fellows Yates	d46ddd972c	Expand tests and fix schema after review	2022-04-05 11:04:30 +02:00
James A. Fellows Yates	3d662d2e06	Merge branch 'dev' into complexity-filter-bbduk	2022-04-04 21:19:36 +02:00
sofstam	d897c922b2	Add centrifuge classificatioN	2022-04-04 13:51:51 +02:00
James A. Fellows Yates	b2e29ea23a	Merge branch 'dev' into hostremoval	2022-04-03 17:24:07 +02:00
James Fellows Yates	066ceb2bca	Remove flagstat as bowtie2 reports this itself	2022-04-03 17:23:14 +02:00
James Fellows Yates	02d950c58c	Fix test so complexity filter actually executes	2022-04-02 17:18:20 +02:00
James Fellows Yates	7f1a7fb4e7	Add complexity filtering to test profile	2022-04-02 17:05:54 +02:00
Moritz E. Beber	817678d870	chore: add metaphlan3 run to test profile	2022-04-02 15:00:26 +02:00
James Fellows Yates	04fb6f4127	Use new resources for test data	2022-03-28 20:38:16 +02:00
James Fellows Yates	94e5cfef4a	Filter long reads for MALT, bump cpus for FastQC for minigut to pass	2022-03-28 18:20:10 +02:00
sofstam	37a70dc3e3	Merge branch 'dev' into classification_centrifuge	2022-03-25 16:18:35 +01:00
James Fellows Yates	dfcf8f7b1a	Prettier	2022-03-25 15:10:52 +01:00
sofstam	3ff54e620e	Add centrifuge classification	2022-03-24 13:02:25 +01:00
James A. Fellows Yates	038a8d106a	Fix test with correct URL	2022-03-23 11:25:47 +01:00
James Fellows Yates	48b6ef508d	Update path to samplesheet	2022-03-23 10:06:01 +01:00