977 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
James Fellows Yates	577d270423	Deactivate saving of reads and other large files for full tests	2023-03-17 10:14:40 +01:00
James A. Fellows Yates	66a98c2bc8	Merge pull request #265 from genomic-medicine-sweden/dev ... Update changelog after release	2023-03-13 12:56:40 +01:00
sofstam	1347f27c11	Update changelog after release	2023-03-13 12:21:37 +01:00
James A. Fellows Yates	eaef6ac9bc	Apply suggestions from code review	2023-03-13 10:57:36 +01:00
Sofia Stamouli	ae3ee470ee	Merge pull request #264 from sofstam/update_taxpasta_version ... Updata taxpasta 0.2.3	2023-03-13 10:25:55 +01:00
Sofia Stamouli	0007c99d1c	Merge branch 'dev' into update_taxpasta_version	2023-03-13 09:38:10 +01:00
sofstam	8ecb655952	Prettier	2023-03-13 09:11:53 +01:00
sofstam	213f4e4f23	Updata taxpasta	2023-03-13 08:58:59 +01:00
James A. Fellows Yates	3c4ee927e3	Merge pull request #263 from nf-core/docs-updates ... Update docs based on feedback and add missing results directories	2023-03-12 12:10:34 +01:00
James A. Fellows Yates	9550c76c25	Update README.md	2023-03-12 11:11:05 +01:00
James A. Fellows Yates	7f6e162e1c	Update docs/output.md ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-12 11:08:37 +01:00
James A. Fellows Yates	6266ee782d	Update README.md ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-12 11:08:31 +01:00
James Fellows Yates	95f9bf1fa9	Update credits section	2023-03-12 08:43:56 +01:00
James Fellows Yates	e49668005f	Update docs based on feedback and add missing results directories	2023-03-12 08:35:45 +01:00
Moritz E. Beber	efa398edab	Merge pull request #258 from nf-core/clone-maps ... refactor: double check maps and validation	2023-03-11 21:39:49 +01:00
James A. Fellows Yates	5e400c8c89	Apply suggestions from code review	2023-03-11 20:06:59 +01:00
Moritz E. Beber	bb7323e25d	fix: restore setting id on FASTQ meta	2023-03-11 11:34:47 +01:00
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