118 commits

Author	SHA1	Message	Date
Moritz E. Beber	246da8a7b0	chore: remove fixme comments	2023-03-11 11:28:42 +01:00
Moritz E. Beber	7c1133efb8	add more comments and slight style changes	2023-03-11 11:28:42 +01:00
James Fellows Yates	6e64c2b5a9	Fix copy paste error	2023-03-06 10:50:36 +01:00
James Fellows Yates	735212c9ee	Fix the non-updated KAIJU2TABLE name	2023-03-06 10:47:36 +01:00
James Fellows Yates	a5138ed6e0	Fix ugly warn when KAIJU2TABLE not run	2023-03-06 08:17:50 +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	7dfcdd015b	Re-add the 'native' combined kaiju output	2023-02-16 14:02:13 +01:00
James Fellows Yates	79b4db9a34	Move kaiju2table to profiling	2023-02-16 13:39:05 +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	fe3d42ffd7	Make bracken db_params be a semi-colon separate list to allow kraken and bracken parameters	2023-02-08 13:34:36 +01:00
James Fellows Yates	18886c0cbc	Start trying a different method with maps in profiling	2023-02-07 15:51:25 +01:00
James A. Fellows Yates	4289e1f901	Remove metaphlan3 nanopore filter as _sometimes_ it can work	2023-01-24 15:42:14 +01:00
James A. Fellows Yates	00178d3431	Merge pull request #221 from nf-core/metaphlan3-filter-nanopore ... Filter out nanopore data prior Metaphlan3	2023-01-24 14:39:02 +01:00
James Fellows Yates	14826d5205	Separate conditions, remove some left-over dumps	2023-01-24 13:20:58 +01:00
James Fellows Yates	0358489be0	Remove metaphlan profiling for nanopore as it appears to always result in 100% unclassified	2023-01-24 13:05:52 +01:00
James Fellows Yates	9205831273	Start adding filter for long read and MP3	2023-01-24 11:50:10 +01:00
James Fellows Yates	606ffc0eb1	Remove platform specificity for MALT	2023-01-20 13:40:59 +01:00
James Fellows Yates	460f3ca157	Add database sheet validation	2022-12-12 11:03:40 +01:00
James Fellows Yates	0dccfddc24	Switch order back	2022-12-03 21:38:25 +01:00
James A. Fellows Yates	cf8ad96771	Update subworkflows/local/profiling.nf	2022-12-02 15:09:08 +01:00
James Fellows Yates	ab42f6b662	wteak message	2022-12-02 12:49:00 +01:00
James Fellows Yates	a3cd188b1f	Merge branch 'sep-krakenuniq-test' of github.com:nf-core/taxprofiler into sep-krakenuniq-test	2022-12-02 12:48:18 +01:00
James Fellows Yates	de74e4f727	Fix centrifuge warning, filter out long reads from Brakcen, add some caveat docs to usage.md	2022-12-02 12:47:14 +01:00
James A. Fellows Yates	a34b240dfc	Merge pull request #174 from nf-core/malt-update ... Update MALT	2022-12-01 13:58:30 +01:00
James Fellows Yates	d7fbe55849	Add KU to the test profiles and add id to KU processes	2022-11-29 14:19:01 +01:00
Moritz E. Beber	ddcf38de22	refactor: make mappings explicit	2022-11-29 10:14:20 +01:00
James Fellows Yates	9feb6c2db6	Update MALT	2022-11-24 14:44:04 +01:00
James Fellows Yates	06659af777	Remove flatten	2022-11-22 13:36:40 +01:00
James Fellows Yates	ebfc84e235	Does the grouping work if we have meta?	2022-11-22 13:26:54 +01:00
James Fellows Yates	21759807f7	Does flatten work?	2022-11-22 12:48:54 +01:00
James Fellows Yates	3102e40052	dump teh db	2022-11-22 12:46:26 +01:00
James Fellows Yates	557f2a4d96	Extra dump	2022-11-22 12:26:46 +01:00
James Fellows Yates	5caebcc6ab	Append to correct db	2022-11-22 12:21:59 +01:00
James Fellows Yates	52fc00802b	Correct meta name for db meta	2022-11-22 12:19:56 +01:00
James Fellows Yates	b8937748d3	Fix meta.id isssue	2022-11-22 12:18:52 +01:00
James Fellows Yates	db334c5185	Fix missing info	2022-11-22 12:17:08 +01:00
James Fellows Yates	0f298dca43	group krakenuniq reads by pairs or single end	2022-11-22 12:13:08 +01:00
James Fellows Yates	461482d22a	Try again wit hthe corret param	2022-11-03 15:02:22 +01:00
James Fellows Yates	93f38b14a8	Save report	2022-11-03 15:01:00 +01:00
James Fellows Yates	21a76c2449	Fix cardinality issue	2022-11-03 14:56:26 +01:00
Mahwash Jamy	3147a80a56	Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module	2022-10-31 15:36:57 +00:00
Moritz E. Beber	e658fab430	fix: remove def ... No idea why, must have something to do with scope.	2022-10-27 11:50:47 +02:00
Moritz E. Beber	dd1a4ff158	refactor: only combine same database name ... [skip ci]	2022-10-27 11:19:14 +02:00
Mahwash Jamy	86ca71cfd4	include krakenuniq in profiling subworkflow	2022-10-25 09:45:05 +00:00
Moritz E. Beber	ca7dc308cb	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-10-21 16:36:35 +02:00
Moritz E. Beber	385507ec6f	refactor: use tool name 'bracken' only	2022-10-21 10:03:36 +02:00
Moritz E. Beber	b73b479860	refactor: handle combined kraken2+bracken tool column	2022-10-19 16:21:36 +02:00
Moritz E. Beber	563b34c9c3	refactor: rename process to kraken2	2022-10-14 14:48:27 +02:00
Moritz E. Beber	95621ebd8a	fix: include local module	2022-10-14 14:47:08 +02:00
Moritz E. Beber	ca38d002de	feat: integrate Bracken into the profiling pipeline	2022-10-14 12:18:07 +02:00