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Author	SHA1	Message	Date
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
Sofia Stamouli	c56c6ea694	Merge pull request #176 from nf-core/update_motus ... Include NCBI taxid, read counts and mgc arguments in motus	2022-12-02 12:18:58 +01:00
Sofia Stamouli	7e7299203c	Set values to false	2022-12-02 08:55:23 +01:00
sofstam	6d140c683a	Merge branch 'dev' into update_motus	2022-12-01 18:49:23 +01:00
James A. Fellows Yates	80c25008d0	Merge pull request #177 from nf-core/sep-krakenuniq-test ... Separate KrakenUniq test run	2022-12-01 17:34:30 +01:00
nf-core-bot	410196c37b	[automated] Fix linting with Prettier	2022-12-01 14:33:34 +00:00
sofstam	4800a5f03e	Update schema	2022-12-01 14:23:40 +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	f960c14caf	Fix typos	2022-12-01 13:46:57 +01:00
sofstam	38a818fd17	Apply review suggestions	2022-12-01 13:42:21 +01:00
James A. Fellows Yates	ef1d2da179	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-12-01 12:53:34 +01:00
sofstam	1965ade961	Update schema	2022-12-01 11:32:51 +01:00
sofstam	e5bb627402	Apply review suggestions	2022-12-01 11:12:31 +01:00
James Fellows Yates	bc98f5b80f	Separate KrakenUniq test run	2022-12-01 10:37:14 +01:00
nf-core-bot	8067012c01	[automated] Fix linting with Prettier	2022-12-01 09:15:35 +00:00
James A. Fellows Yates	4f6eb6fd75	Merge pull request #153 from mjamy/add-krakenuniq-module ... Add krakenuniq module	2022-12-01 09:03:29 +01:00
sofstam	933b820c19	Apply review suggestions	2022-11-29 16:57:07 +01:00
Sofia Stamouli	e85c75dcba	Merge branch 'dev' into update_motus	2022-11-29 15:12:31 +01:00
sofstam	12dd836e9c	Fix conflict	2022-11-29 15:00:27 +01:00
sofstam	f389029848	Fix merge conflic	2022-11-29 14:38:39 +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
Sofia Stamouli	7e3ece53bd	Update modules.config	2022-11-29 13:31:00 +01:00
Sofia Stamouli	0088b07220	Fix trailing whitespace	2022-11-29 13:28:04 +01:00
James A. Fellows Yates	770a35d7ac	Update conf/modules.config	2022-11-29 12:49:20 +01:00
Sofia Stamouli	ba727a81ae	Fix left-padding spaces	2022-11-29 12:45:14 +01:00
Sofia Stamouli	71b52b9c94	Apply review suggestions	2022-11-29 11:58:23 +01:00
James A. Fellows Yates	3d949a803f	Merge pull request #175 from nf-core/schema-clean ... Fix schema location ofr fastqc/falco option	2022-11-29 11:49:27 +01:00
Sofia Stamouli	fb6be69d7e	Prettier should work now	2022-11-29 11:37:20 +01:00
sofstam	644a29c699	Prettier	2022-11-29 11:34:57 +01:00
sofstam	5254b8d679	Prettier	2022-11-29 11:25:52 +01:00
sofstam	0235ef42ca	Update nextflow_schema.json	2022-11-29 11:15:40 +01:00
sofstam	49af33f68e	Include NCBI_id, read counts and mgc arguments in motus	2022-11-29 11:07:29 +01:00
Moritz E. Beber	af8ce2cbfd	chore: update krakenuniq	2022-11-29 10:27:35 +01:00
James Fellows Yates	d6c0ebb4c6	Prettier	2022-11-29 10:14:33 +01:00
Moritz E. Beber	ddcf38de22	refactor: make mappings explicit	2022-11-29 10:14:20 +01:00
James Fellows Yates	f13185d98b	Fix schema location ofr fastqc/falco option	2022-11-29 10:13:46 +01:00
James A. Fellows Yates	f114cc4122	Apply suggestions from code review	2022-11-24 16:55:19 +01:00
James A. Fellows Yates	17b1e3df1c	Update test.config	2022-11-24 16:53:39 +01:00
James Fellows Yates	a20b3e3c58	Try to reduce MALT memory	2022-11-24 15:51:12 +01:00
James Fellows Yates	131b39aa8b	Fix linting	2022-11-24 15:49:06 +01:00
James Fellows Yates	9feb6c2db6	Update MALT	2022-11-24 14:44:04 +01:00
Sofia Stamouli	f8b769a8f0	Merge pull request #172 from genomic-medicine-sweden/update_samtools_stats ... Include the mapped reads in samtools stats	2022-11-23 10:21:47 +01:00
sofstam	481f90589c	Apply review suggestions	2022-11-23 09:08:22 +01:00
Moritz E. Beber	b6f5930b49	Merge pull request #171 from nf-core/chore-fail-slow ... chore: let all tests run to completion	2022-11-22 19:22:14 +01:00
sofstam	30af26a8b3	Include the mapped reads in samtools stats	2022-11-22 16:50:50 +01:00
James Fellows Yates	a383c9ae40	Remove the join	2022-11-22 13:39:21 +01:00
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