James A. Fellows Yates
|
cdb21d17b3
|
Merge branch 'dev' into metaphlan3/mergemetaphlantables
|
2022-09-15 13:08:57 +02:00 |
|
James A. Fellows Yates
|
d9795a4fdc
|
Merge pull request #130 from nf-core/krakentools/combinekreports
Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU
|
2022-09-15 13:00:07 +02:00 |
|
James Fellows Yates
|
19a195ed14
|
Append profiler to resulting file
|
2022-09-15 12:30:39 +02:00 |
|
James Fellows Yates
|
21ae9d85c3
|
Ensure merge metaphlan3 tables happens on per database basis
|
2022-09-15 12:29:54 +02:00 |
|
James A. Fellows Yates
|
cd83c04c98
|
Merge pull request #135 from nf-core/dev-warning
Update README.md
|
2022-09-15 08:30:41 +02:00 |
|
James A. Fellows Yates
|
23a33a63cc
|
Update README.md
|
2022-09-15 08:11:37 +02:00 |
|
Rafal Stepien
|
5f3eee9a4a
|
Add working version of PEP-nf-core integration
|
2022-09-14 14:28:48 -04:00 |
|
James A. Fellows Yates
|
5414ae2e55
|
Apply suggestions from code review
|
2022-09-14 11:20:40 +02:00 |
|
James Fellows Yates
|
abbbf9c7ab
|
Update to use tar module compatible for our test databases
|
2022-09-14 11:16:28 +02:00 |
|
Sofia Stamouli
|
343a9e8d16
|
Merge pull request #131 from nf-core/FAQs_README
Update usage.md
|
2022-09-14 09:00:17 +02:00 |
|
Sofia Stamouli
|
ded6d7ab1f
|
Update docs/usage.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2022-09-13 18:13:00 +02:00 |
|
Sofia Stamouli
|
0072c29a6f
|
Update docs/usage.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2022-09-13 18:12:14 +02:00 |
|
James Fellows Yates
|
05e9d92444
|
Add centrigue kreports
|
2022-09-13 16:47:19 +02:00 |
|
Sofia Stamouli
|
c664508240
|
Update usage.md
|
2022-09-13 15:56:06 +02:00 |
|
James Fellows Yates
|
c8dbf5be47
|
Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU
|
2022-09-13 15:47:28 +02:00 |
|
James A. Fellows Yates
|
db688575f6
|
Merge pull request #128 from nf-core/fastp-patch-removal
use proper working FASTP module
|
2022-09-09 19:07:12 +02:00 |
|
James Fellows Yates
|
a764bc4807
|
Start works - need updated module though t have meta
|
2022-09-09 13:57:06 +02:00 |
|
James A. Fellows Yates
|
b28052f1ec
|
Remove patch from modules.json
|
2022-09-09 11:15:25 +02:00 |
|
James Fellows Yates
|
f087136ec9
|
use proper working FASTP module
|
2022-09-09 11:12:47 +02:00 |
|
James A. Fellows Yates
|
3fc7f1f0f8
|
Merge pull request #127 from nf-core/module-update
Update all modules
|
2022-09-08 16:23:44 +02:00 |
|
James Fellows Yates
|
60224e9149
|
Patch fastp until I have an OK on the module update
|
2022-09-08 14:25:23 +02:00 |
|
James A. Fellows Yates
|
cc5df924e4
|
Merge branch 'dev' into module-update
|
2022-09-08 13:36:21 +02:00 |
|
James A. Fellows Yates
|
74c164bbcd
|
Merge pull request #126 from nf-core/kaiju2table-move
Kaiju2table move
|
2022-09-08 13:21:27 +02:00 |
|
James Fellows Yates
|
fc26948950
|
Fix MultiQC
|
2022-09-08 12:49:38 +02:00 |
|
James Fellows Yates
|
d11257b330
|
Module update
|
2022-09-08 08:08:36 +02:00 |
|
James Fellows Yates
|
bbd8049ca1
|
Remove duplicated multqic mixing
|
2022-09-07 13:44:08 +02:00 |
|
James A. Fellows Yates
|
6f87c681fd
|
Merge pull request #125 from nf-core/workflow-tube-map
Workflow tube map
|
2022-09-07 12:52:38 +02:00 |
|
James Fellows Yates
|
832d981976
|
Don't have per sample directory as unnecessary if file names are unique with the db in them
|
2022-09-07 12:22:17 +02:00 |
|
James Fellows Yates
|
3a6536b149
|
Add tube map properly
|
2022-09-07 11:22:22 +02:00 |
|
James Fellows Yates
|
175be0075a
|
Add tube map
|
2022-09-07 11:22:06 +02:00 |
|
James Fellows Yates
|
7c5f9d0c24
|
Start work on more merging tools
|
2022-09-06 17:34:45 +02:00 |
|
James A. Fellows Yates
|
8c6f88d1b5
|
Merge pull request #118 from nf-core/motus-test-fix
Fix mOTUs CI and old param warn
|
2022-09-05 10:38:58 +02:00 |
|
James A. Fellows Yates
|
dd194f3f47
|
Fix mOTUs CI and old param warn
|
2022-09-04 15:01:58 +00:00 |
|
James A. Fellows Yates
|
d093de1bd0
|
Merge pull request #117 from nf-core/fix-selector-warns
Fixes process selector warning
|
2022-09-04 16:23:53 +02:00 |
|
James A. Fellows Yates
|
331231ea28
|
Standardise CI execution
|
2022-09-04 14:02:54 +00:00 |
|
James A. Fellows Yates
|
8456f934ed
|
Update subworkflows/local/visualization_krona.nf
|
2022-09-02 16:15:46 +02:00 |
|
James Fellows Yates
|
ef6fd002d4
|
Merge branch 'dev' into fix-selector-warns
|
2022-09-02 14:11:03 +02:00 |
|
James A. Fellows Yates
|
c9a7797682
|
Merge pull request #116 from nf-core/nf-core-template-merge-2.5.1
Important! Template update for nf-core/tools v2.5.1
|
2022-09-02 13:47:39 +02:00 |
|
James Fellows Yates
|
c3427e44b3
|
Try with retries from sarek approach
|
2022-09-02 12:24:29 +02:00 |
|
James Fellows Yates
|
3a33d81e80
|
Black linting I hope
|
2022-09-02 11:55:19 +02:00 |
|
James Fellows Yates
|
7917e1d656
|
Synronise mOTUs CI setup
|
2022-09-02 11:51:18 +02:00 |
|
James Fellows Yates
|
55d7919fa7
|
Revert "Update ci.yml"
This reverts commit 176a0a6280 .
|
2022-09-02 11:48:57 +02:00 |
|
James Fellows Yates
|
c479714a5e
|
Revert "Update ci.yml"
This reverts commit 61560cf065 .
|
2022-09-02 11:48:49 +02:00 |
|
James Fellows Yates
|
8fe7f8bf4b
|
Revert "Fix final linting problems for template merge"
This reverts commit e64b3f85a4 .
|
2022-09-02 11:47:33 +02:00 |
|
James A. Fellows Yates
|
61560cf065
|
Update ci.yml
|
2022-09-02 10:12:27 +02:00 |
|
James A. Fellows Yates
|
176a0a6280
|
Update ci.yml
|
2022-09-02 10:06:20 +02:00 |
|
James A. Fellows Yates
|
e64b3f85a4
|
Fix final linting problems for template merge
|
2022-09-02 06:07:33 +00:00 |
|
James A. Fellows Yates
|
13e9957e14
|
Fixes process selector warning
|
2022-09-02 06:03:05 +00:00 |
|
James A. Fellows Yates
|
169c7437c8
|
Left over from template merge
|
2022-09-01 16:28:05 +02:00 |
|
James A. Fellows Yates
|
8fff741f85
|
Merge branch 'dev' into nf-core-template-merge-2.5.1
|
2022-09-01 16:26:45 +02:00 |
|