160 commits

Author	SHA1	Message	Date
sofstam	04bc978ef6	Remove taxonomy parameter from taxpasta	2023-02-20 11:56:06 +01:00
sofstam	f0aa89cb87	Rename taxpasta parameters and remove samplesheet parameter	2023-02-17 14:47:29 +01:00
sofstam	5ebc22dd29	Add icon in nextflow_schema.json	2023-02-17 12:58:33 +01:00
sofstam	27b7171b96	Apply review suggestions	2023-02-17 09:16:58 +01:00
sofstam	dad64a688d	Add documentation for taxpasta module	2023-02-16 16:33:36 +01:00
sofstam	de6a4214ef	Add taxpasta_merge to taxprofiler	2023-02-16 14:29:52 +01:00
James Fellows Yates	059cd17114	Fix exporting of mapped/unmapped reads for consistency across both short and long reads	2023-02-07 11:43:40 +01:00
sofstam	4123e06981	Apply last review suggestions	2023-02-03 15:54:29 +01:00
sofstam	3e2b181182	Apply review suggestions	2023-02-03 15:42:45 +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
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
nf-core-bot	ab591e01ff	Template update for nf-core/tools version 2.7.2	2022-12-19 12:10:58 +00:00
James Fellows Yates	1ccd0a0767	Merge branch 'dev' into nf-core-template-merge-2.7.1	2022-12-09 10:16:17 +01:00
nf-core-bot	36f3b5723b	Template update for nf-core/tools version 2.7.1	2022-12-08 13:18:23 +00:00
James Fellows Yates	3dba6405c5	Sets correct default for --shortread_qc_mergepairs	2022-12-06 11:47:16 +01:00
Moritz E. Beber	b2088bcbb3	docs: improve description of shortread_qc_includeunmerged	2022-12-04 21:53:38 +01:00
Moritz E. Beber	4529e7e545	refactor: change parameter exclude unmerged to include	2022-12-04 21:36:12 +01:00
sofstam	6d140c683a	Merge branch 'dev' into update_motus	2022-12-01 18:49:23 +01:00
nf-core-bot	410196c37b	[automated] Fix linting with Prettier	2022-12-01 14:33:34 +00:00
sofstam	4800a5f03e	Update schema	2022-12-01 14:23:40 +01:00
sofstam	38a818fd17	Apply review suggestions	2022-12-01 13:42:21 +01:00
sofstam	1965ade961	Update schema	2022-12-01 11:32:51 +01:00
sofstam	e5bb627402	Apply review suggestions	2022-12-01 11:12:31 +01:00
nf-core-bot	8067012c01	[automated] Fix linting with Prettier	2022-12-01 09:15:35 +00:00
James A. Fellows Yates	4f6eb6fd75	Merge pull request #153 from mjamy/add-krakenuniq-module ... Add krakenuniq module	2022-12-01 09:03:29 +01:00
sofstam	933b820c19	Apply review suggestions	2022-11-29 16:57:07 +01:00
Sofia Stamouli	e85c75dcba	Merge branch 'dev' into update_motus	2022-11-29 15:12:31 +01:00
sofstam	12dd836e9c	Fix conflict	2022-11-29 15:00:27 +01:00
sofstam	f389029848	Fix merge conflic	2022-11-29 14:38:39 +01:00
Sofia Stamouli	71b52b9c94	Apply review suggestions	2022-11-29 11:58:23 +01:00
Sofia Stamouli	fb6be69d7e	Prettier should work now	2022-11-29 11:37:20 +01:00
sofstam	644a29c699	Prettier	2022-11-29 11:34:57 +01:00
sofstam	5254b8d679	Prettier	2022-11-29 11:25:52 +01:00
sofstam	0235ef42ca	Update nextflow_schema.json	2022-11-29 11:15:40 +01:00
James Fellows Yates	d6c0ebb4c6	Prettier	2022-11-29 10:14:33 +01:00
James Fellows Yates	f13185d98b	Fix schema location ofr fastqc/falco option	2022-11-29 10:13:46 +01:00
James Fellows Yates	c5e5696f84	Fix parameter name	2022-11-03 14:58:03 +01:00
James Fellows Yates	21a76c2449	Fix cardinality issue	2022-11-03 14:56:26 +01:00
James Fellows Yates	6459d8920f	Linting!	2022-11-03 14:05:43 +01:00
James A. Fellows Yates	1f31f88635	Merge pull request #158 from nf-core/adapterremoval-fix ... Fix adapterremoval adapter conflict and add optional adapter list file	2022-11-03 11:36:14 +01:00
James A. Fellows Yates	24dc2a2cec	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-11-03 10:03:07 +01:00
James Fellows Yates	d487a1ff2f	Addd FASTP adadapter list	2022-11-02 12:39:34 +01:00
Mahwash Jamy	851016e497	Update nextflow_scheme.json	2022-10-31 16:17:40 +00:00
Moritz E. Beber	bf89525bc2	Merge pull request #146 from nf-core/feat-bracken ... add Bracken to the profiling workflow	2022-10-27 17:35:06 +02:00
nf-core-bot	a402ee3be2	[automated] Fix linting with Prettier	2022-10-27 12:20:08 +00:00
James A. Fellows Yates	733d3dc8c5	Apply suggestions from code review	2022-10-27 14:19:28 +02:00
James A. Fellows Yates	76a662ecc5	Fix adapterremoval adapter conflict and add optional adapter list file	2022-10-27 12:17:19 +00:00
Sofia Stamouli	de6816ec49	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-10-25 11:19:16 +02:00