57 commits

Author	SHA1	Message	Date
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 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
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	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	4dcf8c0b02	Prettier	2023-01-17 15:50:10 +01:00
sofstam	024b683671	Update output and usage	2023-01-17 15:38:56 +01:00
Sofia Stamouli	06575b537d	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-01-16 12:59:23 +01:00
Sofia Stamouli	0e3f9f0b9a	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-01-16 12:59:13 +01:00
sofstam	9f21181972	Add documentation for output docs	2023-01-12 15:47:29 +01:00
Sofia Stamouli	33bce738f5	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-01-11 16:50:06 +01:00
Sofia Stamouli	a49a907ad1	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-01-11 16:47:44 +01:00
Sofia Stamouli	953f9585c9	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-01-11 16:47:18 +01:00
Sofia Stamouli	719fc3cf5d	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-01-11 16:46:30 +01:00
Sofia Stamouli	18c15f8a78	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 20:23:38 +01:00
Sofia Stamouli	fb9de1e212	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 20:23:32 +01:00
Sofia Stamouli	8404c28d08	Review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 20:23:26 +01:00
Sofia Stamouli	2e08c873a0	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 17:34:19 +01:00
Sofia Stamouli	0cbd0a8013	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 17:33:35 +01:00
Sofia Stamouli	af7468522a	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 17:33:18 +01:00
Sofia Stamouli	964771c5f2	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 17:33:04 +01:00
Sofia Stamouli	3c33ba66ca	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 17:32:13 +01:00
Sofia Stamouli	af8fd18d97	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 15:44:35 +01:00
Sofia Stamouli	b0a6bdee5a	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 15:43:45 +01:00
Sofia Stamouli	c6710db7a9	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 15:42:41 +01:00
Sofia Stamouli	d7c4554b18	Apply review suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-20 15:42:10 +01:00
Sofia Stamouli	c9e4eba62d	Prettier	2022-12-13 11:26:06 +01:00
sofstam	4756dc7f0d	Update output.md	2022-12-12 17:14:57 +01:00