116 commits

Author	SHA1	Message	Date
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
James Fellows Yates	a0ee82bf43	Add motus/merge and biom support	2022-07-12 11:39:26 +02:00
James Fellows Yates	02c06b9f7b	Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file	2022-06-30 18:33:11 +02:00
Thomas A. Christensen II	4de43040a3	Switch to using raw classifications for Kaiju2Krona	2022-06-28 09:00:41 -05:00
Thomas A. Christensen II	821dd844d8	Add Kaiju profile conversion to visualization workflow	2022-06-27 09:23:20 -05:00
Thomas A. Christensen II	18284e6e32	Add run_krona option to allow skipping Krona chart creation	2022-06-27 08:45:08 -05:00
Thomas A. Christensen II	ad9bc4b7e9	Add the visualization workflow to the main workflow	2022-06-27 08:25:38 -05:00
James Fellows Yates	d48b3be5a7	Tweak DIAMOND save_reads message	2022-06-03 13:55:17 +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	c9581b1796	Merge branch 'dev' into support-aligned-reads	2022-06-02 12:45:29 +02:00
James A. Fellows Yates	a196e0f628	Merge branch 'dev' into add-filtlong	2022-06-02 11:51:26 +02:00
James Fellows Yates	16ec5bf74a	Update parameter names	2022-05-31 20:11:19 +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	77da358e87	Separate dark and light mode logos, add to README and add to MQC report	2022-05-31 12:45:38 +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
Lauri Mesilaakso	b0faeedc60	Update workflows/taxprofiler.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:20:31 +02:00
ljmesi	e3e55f57c2	Fix alignment ... Just made this change to see if the CI tests would fail again or if the failure was just a one of thing.	2022-05-05 14:02:24 +02:00
ljmesi	6618e8cac6	Change param to a more generic name	2022-05-05 13:20:34 +02:00
ljmesi	5e6be52fab	Implement hostremoval	2022-05-03 09:34:27 +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	06b38f3699	Fix crash, add missing versions	2022-04-23 08:36:01 +02:00
James Fellows Yates	cda1274918	Moves ordering of modules/subworkflow versions mixing to before custom_dumpsoftwareversions mix, otherwise not used in collectFile	2022-04-23 06:47:59 +02:00