1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-10 23:33:09 +00:00
Commit graph

759 commits

Author SHA1 Message Date
James A. Fellows Yates
36629b3dde
Merge branch 'dev' into post-usage-draft-tweaks 2023-01-19 10:36:59 +01:00
James A. Fellows Yates
49e4e20f84
Merge pull request #212 from nf-core/classification-v-profiling
Specify the difference between classification/profiling
2023-01-19 10:06:15 +01:00
James A. Fellows Yates
6e43695264
Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
2023-01-19 08:55:23 +01:00
James A. Fellows Yates
6d380fbbff
Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
2023-01-19 08:49:55 +01:00
James Fellows Yates
33d4a84237 Add explicit sentnece about classification/profiling 2023-01-17 15:23:59 +01:00
James A. Fellows Yates
0cda0d2c51
Merge pull request #213 from nf-core/multiqc-update
Updates MultiQC to 1.14 to add support for all our MQC modules!
2023-01-17 13:37:44 +01:00
James Fellows Yates
92dff9b453 Standardise file names using only underscore 2023-01-17 10:58:30 +01:00
James Fellows Yates
480248bcfd Deactivate all classifer columns from general stats 2023-01-17 10:33:35 +01:00
nf-core-bot
11400b016c [automated] Fix linting with Prettier 2023-01-16 14:11:18 +00:00
James Fellows Yates
0947e9b8ca Fix mOTUs issues 2023-01-16 15:09:30 +01:00
James Fellows Yates
c8f6d713a3 Add tool names to end of prefix files for easier distinguishing in general stats 2023-01-16 14:49:44 +01:00
James A. Fellows Yates
b34a021db7
Specify the difference between classification/profiling 2023-01-16 14:43:46 +01:00
James Fellows Yates
d6fa45b500 update MultiQC and include latest modules 2023-01-16 14:39:52 +01:00
James A. Fellows Yates
6dcf619518
Merge pull request #209 from nf-core/module-version-bumps
Update all modules to make templaite compatible
2022-12-23 23:17:17 +01:00
James Fellows Yates
e5c6db96c8 update all modules to make templaite compatible 2022-12-23 17:23:05 +01:00
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