James A. Fellows Yates
|
c765b3f0bc
|
Merge branch 'dev' into allow-targz-motus
|
2023-01-24 15:20:29 +01:00 |
|
James Fellows Yates
|
f940b07dfe
|
Remove changes from other PR
|
2023-01-24 15:15:02 +01:00 |
|
Moritz E. Beber
|
2431bddcbc
|
Merge pull request #222 from nf-core/fix-save-minimap2
fix: correct pattern to publish minimap2 index
|
2023-01-24 14:57:46 +01:00 |
|
James A. Fellows Yates
|
00178d3431
|
Merge pull request #221 from nf-core/metaphlan3-filter-nanopore
Filter out nanopore data prior Metaphlan3
|
2023-01-24 14:39:02 +01:00 |
|
Moritz E. Beber
|
40f1e7b27a
|
fix: correct pattern to publish minimap2 index
|
2023-01-24 14:15:51 +01:00 |
|
James Fellows Yates
|
14826d5205
|
Separate conditions, remove some left-over dumps
|
2023-01-24 13:20:58 +01:00 |
|
James Fellows Yates
|
0358489be0
|
Remove metaphlan profiling for nanopore as it appears to always result in 100% unclassified
|
2023-01-24 13:05:52 +01:00 |
|
James A. Fellows Yates
|
6eafcc6499
|
Try Moritz's trick, assuming validate_db_rows already checks for tool name validity
|
2023-01-24 12:43:34 +01:00 |
|
James A. Fellows Yates
|
38cbfe9a1c
|
Merge pull request #220 from nf-core/sr-lr-guidance
Add comment about recommendation to split SR/LR
|
2023-01-24 11:51:18 +01:00 |
|
James A. Fellows Yates
|
9cf2d8763f
|
[skip ci] Update docs/usage.md
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
|
2023-01-24 11:50:58 +01:00 |
|
James Fellows Yates
|
4df3409f4a
|
Merge branch 'dev' of github.com:nf-core/taxprofiler into allow-targz-motus
|
2023-01-24 11:50:28 +01:00 |
|
James Fellows Yates
|
9205831273
|
Start adding filter for long read and MP3
|
2023-01-24 11:50:10 +01:00 |
|
James A. Fellows Yates
|
03ef6a69f8
|
Merge pull request #215 from nf-core/remove-platform-specificity
Remove platform specificity for MALT
|
2023-01-24 11:47:48 +01:00 |
|
James Fellows Yates
|
085d9e519c
|
[skip ci] add comment about recommendation to split SR/LR
|
2023-01-24 11:39:37 +01:00 |
|
James Fellows Yates
|
2439aa69d0
|
Use specific samplesheet for MALT without LR reads due to GHA memory limits
|
2023-01-24 10:58:03 +01:00 |
|
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 |
|
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 |
|
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 |
|