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Author SHA1 Message Date
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
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