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Author SHA1 Message Date
James Fellows Yates
ab0c62bdc1 Post-release tweaks to usage.md 2022-12-23 16:23:29 +01:00
James A. Fellows Yates
75a95d5ed8
Merge pull request #143 from genomic-medicine-sweden/update_usage
Update usage.md
2022-12-23 15:14:12 +01:00
James A. Fellows Yates
acba31a8d6
Update taxprofiler.nf 2022-12-23 15:08:01 +01:00
James A. Fellows Yates
e586747680
Add missing comma to list 2022-12-23 15:06:26 +01:00
James A. Fellows Yates
2de049399d
Merge pull request #206 from genomic-medicine-sweden/path_params
Add path parameters
2022-12-23 15:05:59 +01:00
sofstam
6ebfdcd017 Add path parameters 2022-12-23 13:40:22 +01:00
Sofia Stamouli
59fd676ab3
Merge pull request #205 from genomic-medicine-sweden/optional_untar
Optional untar on dbs
2022-12-23 13:14:04 +01:00
Sofia Stamouli
41c1ae9d1a
Commit suggestion
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-12-23 12:20:37 +01:00
sofstam
85906ab1cb Optional untar on dbs 2022-12-23 11:25:57 +01:00
Sofia Stamouli
ec9c7cfedc Prettier 2022-12-22 11:10:54 +01:00
Sofia Stamouli
2f291731c1
Merge branch 'nf-core:dev' into update_usage 2022-12-22 11:09:50 +01:00
Sofia Stamouli
1eeb3b337a
Update usage.md 2022-12-22 11:07:09 +01:00
Sofia Stamouli
29978d83b9
Update centrifuge section 2022-12-22 11:03:49 +01:00
Sofia Stamouli
d6e0d404e3
Update docs/usage.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-12-22 09:18:00 +01:00
Sofia Stamouli
ba43b0daa4
Update docs/usage.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-12-21 09:26:38 +01:00
Sofia Stamouli
35b296e5fd
Merge pull request #202 from nf-core/nf-core-template-merge-2.7.2
Important! Template update for nf-core/tools v2.7.2
2022-12-21 09:18:40 +01:00
James A. Fellows Yates
361700550e
Merge pull request #203 from nf-core/kraken-uniq-bump
Bump KrakenUniq version
2022-12-20 21:51:18 +01:00
James A. Fellows Yates
1279437aa1
Apply suggestions from code review 2022-12-20 21:48:08 +01:00
Sofia Stamouli
1706555eff Prettier 2022-12-20 20:10:05 +01:00
James Fellows Yates
612f532fb2 Bump KrakenUniq version 2022-12-20 20:08:12 +01:00
Sofia Stamouli
24a8da2086 Fix linting 2022-12-20 19:59:55 +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
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
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
Sofia Stamouli
a99f89af77 Apply review suggestions 2022-12-12 16:30:28 +01:00