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Author	SHA1	Message	Date
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
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	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	35b7fc26f7	[skip ci]	2022-10-11 17:01:08 +02:00
Sofia Stamouli	f24344c168	Update README.md	2022-10-11 16:30:42 +02:00
Sofia Stamouli	2423c9d87c	Add headers	2022-10-11 15:02:01 +02:00
Sofia Stamouli	dea45c66c2	Add Krona description	2022-10-11 14:59:48 +02:00
James A. Fellows Yates	f25ee17fcf	Merge pull request #141 from nf-core/minimap-patch ... Remove necessity of patch	2022-10-11 12:46:26 +02:00
James Fellows Yates	56bae85755	Remove necessity of patch	2022-10-11 12:38:18 +02:00
Sofia Stamouli	58dffc0c5d	Add KrakenUniq and Filtlong in documentation	2022-10-11 12:36:48 +02:00
James A. Fellows Yates	ff1670169a	Merge pull request #138 from nf-core/nf-core-template-merge-2.6 ... Important! Template update for nf-core/tools v2.6	2022-10-06 13:03:45 +02:00
Moritz E. Beber	5f3dbd28de	fix: patch inputs to correspond to previous version	2022-10-05 13:51:15 +02:00
Moritz E. Beber	180cac0395	fix: adapt to new samtools/view input	2022-10-05 13:49:35 +02:00
Moritz E. Beber	f5af9fd939	fix: adjust import paths to re-organization	2022-10-05 13:40:43 +02:00
Moritz E. Beber	b407fbcdce	chore: force update all modules	2022-10-05 12:24:18 +02:00