177 commits

Author	SHA1	Message	Date
sofstam	102d53bd75	Subsitute samtools/bam2fq with samtools/fastq	2023-03-23 15:30:07 +01:00
James Fellows Yates	b0939c3ae9	Standardised taxon table and mOTU database docs improvement	2023-03-17 21:03:54 +01:00
James A. Fellows Yates	7f6e162e1c	Update docs/output.md ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-12 11:08:37 +01:00
James Fellows Yates	e49668005f	Update docs based on feedback and add missing results directories	2023-03-12 08:35:45 +01:00
James A. Fellows Yates	91a7a03f48	Apply suggestions from code review ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2023-03-07 11:27:19 +01:00
James Fellows Yates	a2a1b9cbf0	Phrasing tweak	2023-03-06 10:42:30 +01:00
James Fellows Yates	4938549d65	Clarify some documentation	2023-03-06 10:41:32 +01:00
James A. Fellows Yates	f0f89eb082	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 14:58:21 +01:00
James Fellows Yates	74a5343524	Add taxpasta to tubemap	2023-03-03 09:11:10 +01:00
James A. Fellows Yates	6c2ce4a1c9	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 08:37:31 +01:00
James Fellows Yates	5c549e5ce3	Remove TODOs and references to under development	2023-03-02 13:49:03 +01:00
Sofia Stamouli	d454ceed86	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 11:00:42 +01:00
Sofia Stamouli	1aef73cda8	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 10:39:44 +01:00
sofstam	2f0c68a833	Last review suggestions	2023-02-27 10:15:42 +01:00
sofstam	78d7001bea	Document the taxonomy parameters	2023-02-24 16:53:49 +01:00
sofstam	211b5f3a68	Apply review suggestions	2023-02-20 11:49:31 +01:00
sofstam	90a5668007	run_malt false in test and add text in output.md	2023-02-17 15:38:36 +01:00
sofstam	604df56fdb	Add a description about the files used by taxpasta	2023-02-17 13:49:13 +01:00
sofstam	08bfa6a1a7	Apply review suggestions for docs	2023-02-17 13:43:38 +01:00
sofstam	27b7171b96	Apply review suggestions	2023-02-17 09:16:58 +01:00
sofstam	c9b521234b	Prettier for docs	2023-02-16 16:38:00 +01:00
sofstam	dad64a688d	Add documentation for taxpasta module	2023-02-16 16:33:36 +01:00
James Fellows Yates	7dfcdd015b	Re-add the 'native' combined kaiju output	2023-02-16 14:02:13 +01:00
James A. Fellows Yates	4e818efe6d	Update docs/output.md ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-02-16 13:45:04 +01:00
James Fellows Yates	79b4db9a34	Move kaiju2table to profiling	2023-02-16 13:39:05 +01:00
James A. Fellows Yates	45ac6fedc2	Merge pull request #237 from nf-core/bracken-params ... Support Kraken and Bracken db_params in database sheet	2023-02-09 10:59:27 +01:00
James A. Fellows Yates	70eb84b8d5	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2023-02-09 08:01:52 +01:00
James Fellows Yates	b3837cce5b	Relax strictness so can supply empty db_params but block if only single parameter with out ;	2023-02-08 15:44:37 +01:00
James Fellows Yates	18886c0cbc	Start trying a different method with maps in profiling	2023-02-07 15:51:25 +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
Sofia Stamouli	ffc884b542	Merge branch 'nf-core:dev' into documentation	2023-02-03 15:22:51 +01:00
James A. Fellows Yates	b4f88a29ce	Update docs/usage.md [skip ci]	2023-02-03 09:46:01 +01:00
James A. Fellows Yates	11a8624b39	Add warning about database parameters [skip ci]	2023-02-03 09:42:20 +01:00
sofstam	5363274867	Add some last documentation	2023-02-02 13:58:48 +01:00
James Fellows Yates	932dc12fb1	Add list of expected tools in MultiQC report [skip ci]	2023-01-31 13:09:53 +01:00
James Fellows Yates	52907dcc26	Prettier	2023-01-31 13:07:07 +01:00
James A. Fellows Yates	b4d01ac226	Formatting tweaks	2023-01-31 10:23:36 +01:00
sofstam	366745bdbe	Prettier in usage	2023-01-31 09:38:43 +01:00
sofstam	5b738ad353	Review + prettier	2023-01-31 09:35:40 +01:00
sofstam	0edef9ea57	Review suggestions + prettier	2023-01-30 11:16:18 +01:00
sofstam	bc2876228c	Apply review suggestions	2023-01-25 15:11:43 +01:00
sofstam	4f8ac72e1f	Add description of each tool	2023-01-25 13:25:33 +01:00
Sofia Stamouli	5d12785ca4	Merge branch 'nf-core:dev' into update_output	2023-01-25 09:47:30 +01:00
James A. Fellows Yates	9cf2d8763f	[skip ci] Update docs/usage.md ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-01-24 11:50:58 +01:00
James Fellows Yates	085d9e519c	[skip ci] add comment about recommendation to split SR/LR	2023-01-24 11:39:37 +01:00
Sofia Stamouli	7d4035d4c7	Add new line in the description of custom file	2023-01-19 13:44:10 +01:00
James A. Fellows Yates	36629b3dde	Merge branch 'dev' into post-usage-draft-tweaks	2023-01-19 10:36:59 +01:00
James A. Fellows Yates	6e43695264	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-01-19 08:55:23 +01:00