138 commits

Author	SHA1	Message	Date
James A. Fellows Yates	b299a25bc7	Merge pull request #286 from nf-core/multiqc-optimisations ... MultiQC Optimisations	2023-04-21 22:44:36 +02:00
James A. Fellows Yates	2140928638	Merge pull request #272 from nf-core/final-reads-saving ... Add 'final reads for profiling' saving mechanism	2023-04-21 15:21:35 +02:00
James A. Fellows Yates	5a09319fb3	Merge branch 'dev' into multiqc-optimisations	2023-04-21 05:58:23 +02:00
James Fellows Yates	1eb951715f	MultiQC optimisations for DIAMOND and Falco	2023-04-20 15:57:57 +02:00
James A. Fellows Yates	0245c4880b	Merge branch 'dev' into final-reads-saving	2023-04-20 14:18:10 +02:00
James A. Fellows Yates	03c3169f10	Replace all instance of exit 1 with error for safety and consistency	2023-04-04 09:41:22 +00:00
James Fellows Yates	6895e45768	Fix a few conditional bugs and related	2023-03-23 15:46:02 +01:00
James Fellows Yates	fbecfb6f33	Fix broken check for host read removal index	2023-03-17 20:47:09 +01:00
James Fellows Yates	5c549e5ce3	Remove TODOs and references to under development	2023-03-02 13:49:03 +01:00
James Fellows Yates	225773000f	Fix channel structure when supplying own host bt2 index	2023-01-31 12:00:48 +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	ab0c62bdc1	Post-release tweaks to usage.md	2022-12-23 16:23:29 +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
sofstam	6ebfdcd017	Add path parameters	2022-12-23 13:40:22 +01:00
Sofia Stamouli	d691b89727	Merge branch 'dev' into nf-core-template-merge-2.7.2	2022-12-20 15:14:41 +01:00
James A. Fellows Yates	25bb4304e8	Merge pull request #187 from nf-core/revert-pep ... Revert PEP validation back to python samplesheet check	2022-12-20 15:03:18 +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	07bd989bc6	Start work on groovy native datbase checks	2022-12-12 10:02:22 +01:00
James Fellows Yates	4b68e95770	Revert PEP validation back to python samplesheet check	2022-12-12 08:49:13 +01:00
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
Moritz E. Beber	4529e7e545	refactor: change parameter exclude unmerged to include	2022-12-04 21:36:12 +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 Fellows Yates	d487a1ff2f	Addd FASTP adadapter list	2022-11-02 12:39:34 +01:00
Sofia Stamouli	1bd6dbfe58	Add samtools stats for long-reads	2022-10-28 11:40:50 +02:00
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
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	d3d4297ca9	Apply review suggestions	2022-10-24 16:28:07 +02:00
Sofia Stamouli	511cb16a61	Apply review suggestions	2022-10-20 16:55:57 +02:00
Sofia Stamouli	8eddb32b88	Add Falco as an alternative to FastQC	2022-10-18 17:43:16 +02:00
Moritz E. Beber	8768a16d63	refactor: turn warning into error	2022-10-17 17:35:41 +02:00
Moritz E. Beber	fd8a0df2a6	refactor: add warning when run_kraken2 is missing	2022-10-17 17:16:21 +02:00
Moritz E. Beber	fdb8a7f740	Merge branch 'devel' into nf-core-template-merge-2.6	2022-10-05 12:21:54 +02:00
nf-core-bot	51bacb00e6	Template update for nf-core/tools version 2.6	2022-10-05 03:30:53 +00:00
Rafal Stepien	bfd260e9c8	Update workflows/taxprofiler.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-28 12:40:43 -04:00
Rafal Stepien	9349346864	Remove --pep parameter and leave just --input	2022-09-16 10:14:01 -04:00
Rafal Stepien	768f9980d8	Add pep_input_base_dir to workflow. Just need to update modules	2022-09-15 12:31:49 -04:00
Rafal Stepien	5f3eee9a4a	Add working version of PEP-nf-core integration	2022-09-14 14:28:48 -04:00
James A. Fellows Yates	cc5df924e4	Merge branch 'dev' into module-update	2022-09-08 13:36:21 +02:00
James Fellows Yates	fc26948950	Fix MultiQC	2022-09-08 12:49:38 +02:00
James Fellows Yates	d11257b330	Module update	2022-09-08 08:08:36 +02:00
James Fellows Yates	bbd8049ca1	Remove duplicated multqic mixing	2022-09-07 13:44:08 +02:00
James Fellows Yates	7c5f9d0c24	Start work on more merging tools	2022-09-06 17:34:45 +02:00
James Fellows Yates	5552c264b9	Remove now unnecessary input validation	2022-08-30 14:14:01 +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	139cf0d6aa	Fix	2022-07-26 10:12:33 +02:00
James A. Fellows Yates	cc3967a3fd	Apply suggestions from code review	2022-07-15 10:51:41 +02:00