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1001 commits

Author SHA1 Message Date
James Fellows Yates
1a148c5d49 Remove double If and format for readability 2023-01-24 10:48:23 +01:00
James A. Fellows Yates
d56e3133f9
Allow databases of all tools to arrive as tar.gz 2023-01-24 10:45:01 +01:00
James Fellows Yates
1c820f21b3 Dont fail on divide by 0 errors on centrifuge 2023-01-20 17:53:55 +01:00
James A. Fellows Yates
d3bad1d720
Merge pull request #214 from nf-core/local-module-template-sync
Sync local modules with latest template module structure
2023-01-20 14:41:11 +01:00
James Fellows Yates
606ffc0eb1 Remove platform specificity for MALT 2023-01-20 13:40:59 +01:00
James Fellows Yates
cac6f54d2d [extra] Fix warn related to recently changed parameter 2023-01-20 13:36:17 +01:00
James Fellows Yates
2d64628552 Fix left-over warns from loca modules 2023-01-20 13:33:43 +01:00
Sofia Stamouli
7d4035d4c7
Add new line in the description of custom file 2023-01-19 13:44:10 +01:00
James A. Fellows Yates
d9003924be
Merge pull request #201 from genomic-medicine-sweden/removo_todo
Remove TODOs from test configs
2023-01-19 13:15:14 +01:00
James A. Fellows Yates
5162240e77
Merge pull request #208 from nf-core/post-usage-draft-tweaks
Post-release tweaks to usage.md
2023-01-19 11:09:54 +01:00
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
Sofia Stamouli
4dcf8c0b02 Prettier 2023-01-17 15:50:10 +01:00
sofstam
024b683671 Update output and usage 2023-01-17 15:38:56 +01:00
James Fellows Yates
33d4a84237 Add explicit sentnece about classification/profiling 2023-01-17 15:23:59 +01:00
Sofia Stamouli
244fe5e30d
Merge branch 'nf-core:dev' into update_output 2023-01-17 14:47:56 +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
Sofia Stamouli
06575b537d
Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-01-16 12:59:23 +01:00
Sofia Stamouli
0e3f9f0b9a
Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-01-16 12:59:13 +01:00
sofstam
9f21181972 Add documentation for output docs 2023-01-12 15:47:29 +01:00
Sofia Stamouli
3b6be07623
Merge branch 'nf-core:dev' into update_output 2023-01-11 16:56:18 +01:00
Sofia Stamouli
33bce738f5
Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-01-11 16:50:06 +01:00
Sofia Stamouli
a49a907ad1
Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-01-11 16:47:44 +01:00
Sofia Stamouli
953f9585c9
Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-01-11 16:47:18 +01:00
Sofia Stamouli
719fc3cf5d
Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-01-11 16:46:30 +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