960 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
Moritz E. Beber	7104b12e3b	Update subworkflows/local/longread_preprocessing.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-03-11 11:28:42 +01:00
Moritz E. Beber	fa1c779536	fix: insert id key again	2023-03-11 11:28:42 +01:00
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
Moritz E. Beber	5380bc18ec	fix: channels should match 1:1 without remaining elements	2023-03-11 11:28:42 +01:00
Moritz E. Beber	07db3c93e2	style: use map addition instead of cloning	2023-03-11 11:28:42 +01:00
Moritz E. Beber	d17dce5590	style: use subMap and early returns	2023-03-11 11:28:42 +01:00
Moritz E. Beber	0bcea6c993	style: use parameter for branch closure	2023-03-11 11:28:42 +01:00
Moritz E. Beber	b90433f3c2	style: use parameters for filter closure	2023-03-11 11:28:42 +01:00
Moritz E. Beber	aa2410a871	style: use named parameters for closure	2023-03-11 11:28:42 +01:00
Moritz E. Beber	c2ad421051	refactor: simplify DB validation	2023-03-11 11:28:42 +01:00
Sofia Stamouli	53db964bcf	Merge pull request #260 from alexhbnr/spelling_mistake_README ... Update README.md	2023-03-10 14:03:58 +01:00
Alex Hübner	f92a405554	Update README.md	2023-03-10 12:36:52 +01:00
James A. Fellows Yates	c1c4180769	Merge pull request #256 from nf-core/reduce-tests ... Reduce number of tests to check just each tool option is tested	2023-03-07 15:30:06 +01:00
James A. Fellows Yates	a77517af0d	Merge pull request #255 from nf-core/config-ordering ... Minor clean ups from second release review	2023-03-07 15:29:32 +01:00
James Fellows Yates	f3ac1d2a21	Update License to match nextflow.conifg [skip ci]	2023-03-07 14:01:09 +01:00
James A. Fellows Yates	6dbeb5913a	Remove left over skips	2023-03-07 13:18:58 +01:00
James A. Fellows Yates	54e8857233	Reduce number of tests to check just each tool option is tested	2023-03-07 13:06:32 +01:00
James Fellows Yates	98bc6910d5	Update authors and remove left over comment	2023-03-07 11:47:54 +01:00
James Fellows Yates	5c8e2b492c	Syncronise local modules with other generic container modules	2023-03-07 11:41:57 +01:00
James A. Fellows Yates	91a7a03f48	Apply suggestions from code review ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2023-03-07 11:27:19 +01:00
James Fellows Yates	e92196cd12	Remove left over comment	2023-03-07 11:10:10 +01:00
James Fellows Yates	8ca9fad3b1	move errorStrategy to config	2023-03-07 11:09:25 +01:00
James Fellows Yates	b5a2983c5f	Make modules entries consistent	2023-03-07 11:06:35 +01:00
Sofia Stamouli	d647e61a2f	Merge pull request #253 from nf-core/futher-further-prerelease-updates ... Futher further prerelease updates: FALCO display in MultiQC	2023-03-06 15:56:50 +01:00
James Fellows Yates	2d9dede6d4	Improve python regex	2023-03-06 12:59:08 +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	a2a1b9cbf0	Phrasing tweak	2023-03-06 10:42:30 +01:00
James Fellows Yates	4938549d65	Clarify some documentation	2023-03-06 10:41:32 +01:00
James Fellows Yates	9ed384e0f2	Collapse FALCO and FASTQC sections, move FALCO/FASTQC sections together	2023-03-06 10:37:09 +01:00
James Fellows Yates	1f1c63bb51	Start fixing FastQC/Falco display in MultiQC	2023-03-06 09:47:26 +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	f0f89eb082	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 14:58:21 +01:00
James A. Fellows Yates	c66c67524c	Update nextflow.config ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 13:33:41 +01:00
James A. Fellows Yates	799a44cb8c	Merge pull request #252 from nf-core/further-prerelease-changes ... Further prerelease changes	2023-03-03 10:16:23 +01:00
James Fellows Yates	6d9cdd3c78	And the other file	2023-03-03 09:15:21 +01:00
James Fellows Yates	5feebf8d69	Fix linting issues	2023-03-03 09:12:11 +01:00
James Fellows Yates	74a5343524	Add taxpasta to tubemap	2023-03-03 09:11:10 +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 A. Fellows Yates	0c9d6cabe8	Merge pull request #250 from nf-core/pre-release-updates ... Cleanup PR for release	2023-03-02 13:54:45 +01:00
James Fellows Yates	ec89187504	Update CHANGELOG for first release	2023-03-02 13:53:32 +01:00
James Fellows Yates	aedf0b34de	Bump version for release	2023-03-02 13:51:28 +01:00
James Fellows Yates	5c549e5ce3	Remove TODOs and references to under development	2023-03-02 13:49:03 +01:00
James Fellows Yates	a14937f668	Remove unused module and fix module structure for samplesheet_check	2023-03-02 13:34:10 +01:00
Sofia Stamouli	d9f687667e	Merge pull request #249 from genomic-medicine-sweden/update_taxpasta ... Update taxpasta	2023-03-02 08:53:38 +01:00
sofstam	7ae7fb528b	Prettier	2023-03-01 22:17:07 +01:00
sofstam	58f09ed659	Update taxpasta/merge module	2023-03-01 22:12:09 +01:00
Sofia Stamouli	b93c7082b8	Merge pull request #248 from genomic-medicine-sweden/update_taxpasta_merge ... Update taxpasta/merge to version 0.2.0 and add taxonomy argument	2023-02-27 15:19:58 +01:00
Sofia Stamouli	df5303270d	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 14:18:30 +01:00