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Author	SHA1	Message	Date
James Fellows Yates	06659af777	Remove flatten	2022-11-22 13:36:40 +01:00
James Fellows Yates	cacd7d3128	Not just in stub	2022-11-22 13:33:13 +01:00
James Fellows Yates	e8de006ed6	With a join	2022-11-22 13:27:49 +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	c5e5696f84	Fix parameter name	2022-11-03 14:58:03 +01:00
James Fellows Yates	c03a21c770	Merge branch 'add-krakenuniq-module' of github.com:mjamy/taxprofiler into add-krakenuniq-module	2022-11-03 14:56:43 +01:00
James Fellows Yates	21a76c2449	Fix cardinality issue	2022-11-03 14:56:26 +01:00
nf-core-bot	0c445759e4	[automated] Fix linting with Prettier	2022-11-03 13:42:39 +00:00
James Fellows Yates	6459d8920f	Linting!	2022-11-03 14:05:43 +01:00
Mahwash Jamy	aecf308840	Update documentation for krakenuniq	2022-10-31 16:41:35 +00:00
Mahwash Jamy	851016e497	Update nextflow_scheme.json	2022-10-31 16:17:40 +00:00
Mahwash Jamy	febcbfc057	add missing parameters to nextflow.config	2022-10-31 16:07:53 +00:00
Mahwash Jamy	3147a80a56	Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module	2022-10-31 15:36:57 +00:00
Sofia Stamouli	074d3ec204	Merge pull request #161 from genomic-medicine-sweden/samtools_stats ... Add samtools stats for long-reads	2022-10-31 10:59:37 +01:00
Sofia Stamouli	f1778acf35	Apply review suggestion	2022-10-31 09:31:13 +01:00
Sofia Stamouli	f87131c7b1	Save samtools stats output	2022-10-28 14:10:24 +02:00
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
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
Moritz E. Beber	0de1ac5356	docs: add Bracken reference	2022-10-27 10:14:57 +02:00
Sofia Stamouli	63c260bfbc	Merge pull request #148 from genomic-medicine-sweden/add_falco ... Add Falco as an alternative to FastQC	2022-10-25 12:40:26 +02:00
Mahwash Jamy	f4717be9ab	add krakenuniq to modules.config	2022-10-25 09:50:44 +00:00
Mahwash Jamy	86ca71cfd4	include krakenuniq in profiling subworkflow	2022-10-25 09:45:05 +00:00
Mahwash Jamy	36e101a78b	Install krakenuniq module	2022-10-25 09:26:33 +00:00
Sofia Stamouli	de6816ec49	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-10-25 11:19:16 +02:00
Sofia Stamouli	7b1a53b062	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-10-25 11:19:08 +02:00
Sofia Stamouli	8c3e80b6ea	Add helptest to nextflow_schema,add versions to longread_preprocessing	2022-10-25 11:13:26 +02:00
nf-core-bot	00038db634	[automated] Fix linting with Prettier	2022-10-25 08:51:58 +00:00
Sofia Stamouli	d3d4297ca9	Apply review suggestions	2022-10-24 16:28:07 +02:00
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	60e369aa5c	fix: set default run bracken to false	2022-10-21 10:47:51 +02:00
Moritz E. Beber	7bd6112133	docs: describe Bracken database usage	2022-10-21 10:18:11 +02:00
Moritz E. Beber	385507ec6f	refactor: use tool name 'bracken' only	2022-10-21 10:03:36 +02:00
Sofia Stamouli	19231538da	Prettier	2022-10-20 16:59:32 +02:00
Sofia Stamouli	511cb16a61	Apply review suggestions	2022-10-20 16:55:57 +02:00
Moritz E. Beber	8deb7757d8	fix: remove Bracken from standardise reports	2022-10-19 16:21:57 +02:00
Moritz E. Beber	b73b479860	refactor: handle combined kraken2+bracken tool column	2022-10-19 16:21:36 +02:00
Moritz E. Beber	c7c7a7f678	refactor: change Bracken prefix to be more specific	2022-10-19 16:20:09 +02:00
Sofia Stamouli	7881ba9aef	Fix the amount of left-padding spaces	2022-10-18 17:50:49 +02:00