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Sofia Stamouli
c6710db7a9
Apply review suggestion 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 15:42:41 +01:00
Sofia Stamouli
d7c4554b18
Apply review suggestion 
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
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
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
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
c9e4eba62d Prettier 2022-12-13 11:26:06 +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
James Fellows Yates
e31e7d3172 Update mOTUs to 3.0.3 2022-12-12 15:42:01 +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
sofstam
c5f4c9486a Start the documentation of output.md 2022-12-09 15:30:11 +01:00
James A. Fellows Yates
13c4f44ca6
Merge pull request #185 from nf-core/nf-core-template-merge-2.7.1 
Important! Template update for nf-core/tools v2.7.1
 2022-12-09 12:58:28 +01:00
James Fellows Yates
dca0b86c78 Fix versions 2022-12-09 10:28:48 +01:00
James Fellows Yates
da3d2d96e6 Fix linting 2022-12-09 10:27:50 +01:00
James Fellows Yates
1ccd0a0767 Merge branch 'dev' into nf-core-template-merge-2.7.1 2022-12-09 10:16:17 +01:00
nf-core-bot
36f3b5723b Template update for nf-core/tools version 2.7.1 2022-12-08 13:18:23 +00:00
James A. Fellows Yates
1687b43596
Merge pull request #183 from nf-core/update-bracken-params 
Update bracken so parameters come directly from database args
 2022-12-07 16:39:52 +01:00
James Fellows Yates
d8751787ac Update bracken so parameters come directly from database args 2022-12-07 07:27:40 +01:00
James Fellows Yates
3dba6405c5 Sets correct default for --shortread_qc_mergepairs 2022-12-06 11:47:16 +01:00
Moritz E. Beber
9064584356
Merge pull request #180 from nf-core/rename-exclude-unmerged 
refactor: change parameter exclude unmerged to include
 2022-12-05 10:53:32 +01:00
Moritz E. Beber
24e5bc5410 refactor: use shorter and more explicit syntax 2022-12-04 21:54:10 +01:00
Moritz E. Beber
b2088bcbb3 docs: improve description of shortread_qc_includeunmerged 2022-12-04 21:53:38 +01:00
Moritz E. Beber
4529e7e545 refactor: change parameter exclude unmerged to include 2022-12-04 21:36:12 +01:00
James A. Fellows Yates
7992edd181
Merge pull request #181 from nf-core/sep-krakenuniq-test 
Filter out Nanopore reads from Bracken
 2022-12-04 13:57:11 +01:00
James Fellows Yates
0a0dffa37c Try separating MALT 2022-12-04 12:06:33 +01:00