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Author	SHA1	Message	Date
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
James A. Fellows Yates	10f7f9e5de	Merge branch 'adapterremoval-fix' of https://github.com/nf-core/taxprofiler into adapterremoval-fix	2022-10-27 12:23:52 +00:00
James A. Fellows Yates	08d61065e5	Add adapterlist to AR2 subworkflow	2022-10-27 12:23:27 +00:00
nf-core-bot	a402ee3be2	[automated] Fix linting with Prettier	2022-10-27 12:20:08 +00:00
James A. Fellows Yates	733d3dc8c5	Apply suggestions from code review	2022-10-27 14:19:28 +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
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
Sofia Stamouli	0481bb9449	Prettier	2022-10-18 17:48:40 +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	48b00b7d62	refactor: create standardized Bracken reports	2022-10-17 17:33:24 +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	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
James A. Fellows Yates	4f27998852	Update usage.md	2022-10-14 14:37:52 +02:00
Moritz E. Beber	9dc819ceff	style: reformat schema	2022-10-14 13:16:54 +02:00
Moritz E. Beber	c4f6468275	chore: update parameters schema	2022-10-14 12:55:26 +02:00
Moritz E. Beber	7f8180f458	fix: emit tool versions	2022-10-14 12:49:07 +02:00
Moritz E. Beber	767663d975	chore: add Bracken to test configs	2022-10-14 12:18:55 +02:00
Moritz E. Beber	ca38d002de	feat: integrate Bracken into the profiling pipeline	2022-10-14 12:18:07 +02:00
Moritz E. Beber	4f728648f5	feat: add process to standardize kraken report	2022-10-14 10:56:14 +02:00
Moritz E. Beber	4352d35937	chore: install Bracken module	2022-10-14 10:52:17 +02:00
Sofia Stamouli	e98cd038c7	[skip ci] ... Add description for MALT	2022-10-12 12:56:54 +02:00
Sofia Stamouli	0b16010b92	Add tutorials section	2022-10-12 11:39:03 +02:00
Sofia Stamouli	4e771ab2c7	Merge pull request #142 from genomic-medicine-sweden/update_readme ... Add KrakenUniq and Filtlong in documentation	2022-10-12 11:38:01 +02:00
Sofia Stamouli	bd56bc0ed6	Add minimap2 and update contributors	2022-10-12 11:10:53 +02:00
Sofia Stamouli	d09a8e0545	[skip ci]	2022-10-11 17:44:48 +02:00