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Sofia Stamouli
964771c5f2
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 17:33:04 +01:00
Sofia Stamouli
3c33ba66ca
Apply review suggestion 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 17:32:13 +01:00
Sofia Stamouli
af8fd18d97
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 15:44:35 +01:00
Sofia Stamouli
b0a6bdee5a
Apply review suggestion 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 15:43:45 +01:00
Sofia Stamouli
c6710db7a9
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 15:42:41 +01:00
Sofia Stamouli
d7c4554b18
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 15:42:10 +01:00
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