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Author SHA1 Message Date
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
Sofia Stamouli
fff7453d0c
Update nextflow_schema.json 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-02-27 14:18:22 +01:00
Sofia Stamouli
9621d34c4a
Update nextflow_schema.json 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-02-27 14:18:11 +01:00
Sofia Stamouli
54af021965
Update nextflow_schema.json 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-02-27 14:18:01 +01:00
sofstam
99fe8adb1b Add helptext 2023-02-27 13:49:02 +01:00
sofstam
c94bfb0cf1 Fix prettier 2023-02-27 13:09:07 +01:00
sofstam
4dea308c22 Linting 2023-02-27 11:34:19 +01:00
Sofia Stamouli
69430ef851
Update nextflow.config 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-02-27 11:02:55 +01:00
Sofia Stamouli
e3e465df1f
Update nextflow_schema.json 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-02-27 11:00:59 +01:00
Sofia Stamouli
d454ceed86
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-02-27 11:00:42 +01:00
Sofia Stamouli
1aef73cda8
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-02-27 10:39:44 +01:00
Sofia Stamouli
d96e0a17a5
Update conf/modules.config 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-02-27 10:39:10 +01:00
sofstam
489650feb8 Linting 2023-02-27 10:24:14 +01:00
sofstam
2f0c68a833 Last review suggestions 2023-02-27 10:15:42 +01:00
sofstam
78d7001bea Document the taxonomy parameters 2023-02-24 16:53:49 +01:00
sofstam
a7ae57c94e Fix linting 2023-02-24 15:53:54 +01:00
sofstam
e18e68faa5 Apply review suggestion 2023-02-24 15:50:24 +01:00
sofstam
5dc3cbc278 Rename taxonomy argument 2023-02-24 13:04:38 +01:00
sofstam
5a6fcf1f42 Update taxpasta/merge to version 0.2.0 and add taxonomy argument 2023-02-24 11:44:07 +01:00
James A. Fellows Yates
78c2d275e6
Merge pull request #245 from nf-core/ku-docs [skip ci] 
Fix typo in schema docs [skip ci]
 2023-02-23 14:35:54 +01:00
James Fellows Yates
cd4614f387 Fix typo in schema docs [skip ci] 2023-02-23 14:00:00 +01:00
James A. Fellows Yates
91255b4d2d
Merge pull request #244 from nf-core/taxpasta-ku-fix 
Fix KrakenUniq Taxpasta issue
 2023-02-22 14:20:06 +01:00
James A. Fellows Yates
32c0d8d6a5
Fix KrakenUniq Taxpasta issue 2023-02-22 08:24:48 +01:00
James A. Fellows Yates
877f6ca8b3
Merge pull request #243 from nf-core/rma2info-label-fix 
Fix label base.config for MEGAN_RMA2INFO
 2023-02-20 21:46:32 +01:00