Sofia Stamouli
|
3eb6a29fb0
|
Merge branch 'nf-core:dev' into update_output
|
2022-12-20 15:30:19 +01:00 |
|
Sofia Stamouli
|
d691b89727
|
Merge branch 'dev' into nf-core-template-merge-2.7.2
|
2022-12-20 15:14:41 +01:00 |
|
James A. Fellows Yates
|
25bb4304e8
|
Merge pull request #187 from nf-core/revert-pep
Revert PEP validation back to python samplesheet check
|
2022-12-20 15:03:18 +01:00 |
|
Sofia Stamouli
|
7be3cfc450
|
Review suggestions
|
2022-12-20 15:00:17 +01:00 |
|
Sofia Stamouli
|
502a4a81cd
|
Merge branch 'nf-core:dev' into update_usage
|
2022-12-20 14:11:05 +01:00 |
|
James Fellows Yates
|
656956b0f9
|
Black formatting
|
2022-12-20 14:08:42 +01:00 |
|
James Fellows Yates
|
577da7e835
|
Remove .first() as the module only executes once anyway and we get a ugly warning
|
2022-12-20 13:59:14 +01:00 |
|
James A. Fellows Yates
|
41063bc670
|
Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
|
2022-12-20 13:56:01 +01:00 |
|
James Fellows Yates
|
11db981a88
|
minor fixes
|
2022-12-20 13:55:15 +01:00 |
|
James A. Fellows Yates
|
7709245874
|
Update subworkflows/local/input_check.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
|
2022-12-20 13:54:05 +01:00 |
|
nf-core-bot
|
ab591e01ff
|
Template update for nf-core/tools version 2.7.2
|
2022-12-19 12:10:58 +00:00 |
|
Sofia Stamouli
|
c23eb968f9
|
Remove TODOs from test configs
|
2022-12-16 15:20:06 +01:00 |
|
Sofia Stamouli
|
b5c72894fd
|
Merge pull request #194 from nf-core/multiqc_config
Configuration of multiqc report
|
2022-12-16 13:42:55 +01:00 |
|
Sofia Stamouli
|
07a1cfae62
|
Update assets/multiqc_config.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2022-12-16 11:46:42 +01:00 |
|
Sofia Stamouli
|
5a592f086e
|
Update assets/multiqc_config.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2022-12-16 11:46:35 +01:00 |
|
Sofia Stamouli
|
a2c81e33fd
|
Prettier
|
2022-12-16 08:38:58 +01:00 |
|
Sofia Stamouli
|
d6db04503e
|
Configuration of multiqc report
|
2022-12-15 17:04:45 +01:00 |
|
James A. Fellows Yates
|
aa117e8af9
|
Merge pull request #192 from nf-core/publishing-fix
Fix publishing of log files of rpreprocessing steps
|
2022-12-15 14:39:55 +01:00 |
|
James Fellows Yates
|
0bdc119f9c
|
Include falco patch
|
2022-12-15 13:27:41 +01:00 |
|
James Fellows Yates
|
9e6a91aff9
|
Distinguish Kraken2 from Bracken
|
2022-12-15 13:25:01 +01:00 |
|
James Fellows Yates
|
3b86a22556
|
Fix falco publication names
|
2022-12-15 12:57:49 +01:00 |
|
James Fellows Yates
|
88589fbc53
|
Fix publishing of log files of rpreprocessing steps
|
2022-12-15 10:35:06 +01:00 |
|
Sofia Stamouli
|
644c4ab831
|
Review suggestions
|
2022-12-13 12:00:32 +01:00 |
|
Sofia Stamouli
|
3282f5944b
|
Apply prettier
|
2022-12-13 11:28:17 +01:00 |
|
Sofia Stamouli
|
c9e4eba62d
|
Prettier
|
2022-12-13 11:26:06 +01:00 |
|
sofstam
|
d99706f43d
|
Move database section and alphabetical order
|
2022-12-13 11:23:07 +01:00 |
|
Sofia Stamouli
|
f80adee9e2
|
Review suggestions and prettier
|
2022-12-13 09:50:05 +01:00 |
|
Sofia Stamouli
|
1eb3da758b
|
Apply review suggestion
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2022-12-13 09:38:09 +01:00 |
|
Sofia Stamouli
|
97e48075c8
|
Apply review suggestion
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2022-12-13 09:37:43 +01:00 |
|
James A. Fellows Yates
|
578081df2e
|
Merge pull request #189 from nf-core/database-check
Adds (native groovy!) database check
|
2022-12-13 08:43:00 +01:00 |
|
James A. Fellows Yates
|
971f6a6ea8
|
Merge pull request #190 from nf-core/motus-update-version
Update mOTUs to 3.0.3
|
2022-12-12 18:24:05 +01:00 |
|
sofstam
|
4756dc7f0d
|
Update output.md
|
2022-12-12 17:14:57 +01:00 |
|
sofstam
|
b1eb477f33
|
Update output.md
|
2022-12-12 17:06:05 +01:00 |
|
Sofia Stamouli
|
a99f89af77
|
Apply review suggestions
|
2022-12-12 16:30:28 +01:00 |
|
James Fellows Yates
|
e31e7d3172
|
Update mOTUs to 3.0.3
|
2022-12-12 15:42:01 +01:00 |
|
Sofia Stamouli
|
bd5cd0a897
|
Prettier
|
2022-12-12 13:34:53 +01:00 |
|
sofstam
|
896a39e68d
|
Apply review suggestions
|
2022-12-12 13:19:59 +01:00 |
|
James A. Fellows Yates
|
be85cb408c
|
Merge pull request #188 from nf-core/bracken-mergetables
Add Bracken mergetables
|
2022-12-12 11:26:19 +01:00 |
|
James Fellows Yates
|
7c66968fef
|
More comments
|
2022-12-12 11:04:21 +01:00 |
|
James Fellows Yates
|
460f3ca157
|
Add database sheet validation
|
2022-12-12 11:03:40 +01:00 |
|
James Fellows Yates
|
3df0a383da
|
Update combine bracken outputs to include meta for publishing purposes
|
2022-12-12 10:10:24 +01:00 |
|
James Fellows Yates
|
07bd989bc6
|
Start work on groovy native datbase checks
|
2022-12-12 10:02:22 +01:00 |
|
sofstam
|
c9a6320dac
|
Merge branch 'update_output' of https://github.com/genomic-medicine-sweden/taxprofiler into update_output
Conflicts:
docs/output.md
|
2022-12-12 09:13:02 +01:00 |
|
James Fellows Yates
|
4b68e95770
|
Revert PEP validation back to python samplesheet check
|
2022-12-12 08:49:13 +01:00 |
|
James Fellows Yates
|
8939ce3e20
|
Start adding bracken/combinebrackenreports (need smodule update)
|
2022-12-11 16:52:34 +01:00 |
|
sofstam
|
b35d26744d
|
Add classifiers
|
2022-12-09 17:11:48 +01:00 |
|
Sofia Stamouli
|
6d0b5d0a58
|
Prettier
|
2022-12-09 15:38:59 +01:00 |
|
Sofia Stamouli
|
98f3ab9fd1
|
Apply prettier
|
2022-12-09 15:35:51 +01:00 |
|
sofstam
|
c5f4c9486a
|
Start the documentation of output.md
|
2022-12-09 15:30:11 +01:00 |
|
Sofia Stamouli
|
a622dcaef0
|
Delete one line
|
2022-12-09 13:59:37 +01:00 |
|