ljmesi
|
58d4dec70b
|
Update samtools view
|
2022-05-03 11:09:54 +02:00 |
|
ljmesi
|
17039ebc6b
|
Fix type to boolean for flags
|
2022-05-03 11:07:23 +02:00 |
|
ljmesi
|
4b2a3789cd
|
Update default values for host removal parameters
|
2022-05-03 11:03:48 +02:00 |
|
ljmesi
|
fa1c132635
|
Update nextflow_schema
|
2022-05-03 11:03:25 +02:00 |
|
ljmesi
|
afdebaf09a
|
Remove own modification to a module
|
2022-05-03 10:15:11 +02:00 |
|
ljmesi
|
5e6be52fab
|
Implement hostremoval
|
2022-05-03 09:34:27 +02:00 |
|
ljmesi
|
a821f748ee
|
Add modules
|
2022-05-03 09:28:46 +02:00 |
|
James A. Fellows Yates
|
2bae9d58ee
|
Merge pull request #72 from nf-core/diamond
Add DIAMOND
|
2022-04-30 20:28:28 +02:00 |
|
James Fellows Yates
|
0630fce3b5
|
Tweak based on official DIAMOND test-data
|
2022-04-30 08:11:40 +02:00 |
|
James Fellows Yates
|
a4a9b161d8
|
Lintin
|
2022-04-29 22:02:44 +02:00 |
|
James Fellows Yates
|
8126d16dee
|
Add draft version of DIAMOND
|
2022-04-29 21:59:42 +02:00 |
|
Sofia Stamouli
|
120f86e5c7
|
Merge pull request #67 from genomic-medicine-sweden/classification_kaiju2table
Add kaiju2table to taxprofiler
|
2022-04-26 16:11:47 +02:00 |
|
Sofia Stamouli
|
194b89e66a
|
Prettier
|
2022-04-26 12:53:39 +02:00 |
|
Sofia Stamouli
|
7afda265c5
|
Enumerating taxon
|
2022-04-26 11:27:18 +02:00 |
|
Sofia Stamouli
|
f4480feb9b
|
Prettier
|
2022-04-25 17:45:26 +02:00 |
|
sofstam
|
d082d67bcb
|
Add kaiju2table to taxprofiler
|
2022-04-25 17:36:29 +02:00 |
|
James A. Fellows Yates
|
bc84afe80d
|
Merge pull request #66 from nf-core/versions-fix
Fix version reporting
|
2022-04-25 16:38:28 +02:00 |
|
Sofia Stamouli
|
1c694145d4
|
Merge pull request #65 from genomic-medicine-sweden/classification_kreport
Add centrifuge kreport in taxprofiler
|
2022-04-25 10:14:43 +02:00 |
|
Sofia Stamouli
|
e3a613de00
|
Prettier
|
2022-04-25 09:32:25 +02:00 |
|
Sofia Stamouli
|
d8a5c793e2
|
Remove parameter from nextflow_schema
|
2022-04-25 09:29:43 +02:00 |
|
Sofia Stamouli
|
ba2479b95b
|
Prettier
|
2022-04-25 09:26:49 +02:00 |
|
Sofia Stamouli
|
e7e24c2d95
|
Prettier and suggestions from review
|
2022-04-25 09:21:29 +02:00 |
|
James Fellows Yates
|
06b38f3699
|
Fix crash, add missing versions
|
2022-04-23 08:36:01 +02:00 |
|
James Fellows Yates
|
cda1274918
|
Moves ordering of modules/subworkflow versions mixing to before custom_dumpsoftwareversions mix, otherwise not used in collectFile
|
2022-04-23 06:47:59 +02:00 |
|
sofstam
|
c00ca1c2b8
|
Add centrifuge kreport in taxprofiler
|
2022-04-22 15:24:10 +02:00 |
|
James A. Fellows Yates
|
63230c3254
|
Merge pull request #63 from nf-core/maxforks
Update test.config to only allow maxFork to 1 for MALT_RUN
|
2022-04-21 12:57:37 +02:00 |
|
James A. Fellows Yates
|
47a34d4c7e
|
Merge pull request #59 from nf-core/hostremoval-publish-fix
Add finer control over for hostremoval saving
|
2022-04-21 12:57:09 +02:00 |
|
James A. Fellows Yates
|
cd3c8f6a89
|
Merge branch 'dev' into hostremoval-publish-fix
|
2022-04-21 11:43:06 +02:00 |
|
James A. Fellows Yates
|
d850333e11
|
Linting
|
2022-04-20 13:42:26 +02:00 |
|
James A. Fellows Yates
|
d031322c16
|
Update test.config
|
2022-04-20 13:41:01 +02:00 |
|
Sofia Stamouli
|
e71e7b86a2
|
Merge pull request #53 from genomic-medicine-sweden/classification_kaiju
Add kaiju/kaiju in taxprofiler
|
2022-04-20 10:57:00 +02:00 |
|
Sofia Stamouli
|
236141f065
|
Resolve conflicts with dev
|
2022-04-20 10:17:10 +02:00 |
|
James A. Fellows Yates
|
571495c812
|
Merge pull request #60 from nf-core/fasta-filtering
Adds filtering out of FASTA for tools that don't support it
|
2022-04-20 10:11:17 +02:00 |
|
James A. Fellows Yates
|
d16cd75652
|
Merge branch 'dev' into hostremoval-publish-fix
|
2022-04-20 09:53:51 +02:00 |
|
James A. Fellows Yates
|
53d76559af
|
Merge pull request #55 from nf-core/megan-postprocessing
Add MEGAN for MALT postprocessing
|
2022-04-20 09:52:55 +02:00 |
|
James A. Fellows Yates
|
fb5347a9fc
|
Merge pull request #58 from nf-core/docs
Add documentation for preprocessing subworkflows
|
2022-04-20 09:26:53 +02:00 |
|
James Fellows Yates
|
9fd94b1389
|
Switch to string interpolation
|
2022-04-20 09:25:54 +02:00 |
|
James Fellows Yates
|
60d232d62c
|
Revert "Update subworkflows/local/profiling.nf"
This reverts commit b7d0557ee0 .
|
2022-04-20 09:23:38 +02:00 |
|
James A. Fellows Yates
|
ac714dd30f
|
Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
|
2022-04-20 09:22:10 +02:00 |
|
James A. Fellows Yates
|
b7d0557ee0
|
Update subworkflows/local/profiling.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
|
2022-04-20 09:15:45 +02:00 |
|
Sofia Stamouli
|
4e1b1269be
|
Apply prettier
|
2022-04-19 13:11:43 +02:00 |
|
Sofia Stamouli
|
dc276e8bae
|
Merge branch 'nf-core:dev' into classification_kaiju
|
2022-04-19 13:09:15 +02:00 |
|
sofstam
|
1b7ff2265d
|
Update usage.md, reformat test.config and modules.config
|
2022-04-19 13:04:58 +02:00 |
|
James A. Fellows Yates
|
87777a4289
|
Update subworkflows/local/profiling.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
|
2022-04-19 12:54:57 +02:00 |
|
James A. Fellows Yates
|
ecaff371aa
|
Update input_check.nf
|
2022-04-18 07:35:19 +02:00 |
|
James A. Fellows Yates
|
9f634805e4
|
Update subworkflows/local/profiling.nf
|
2022-04-18 07:31:44 +02:00 |
|
James A. Fellows Yates
|
9c3c8f1f4e
|
Merge branch 'dev' into fasta-filtering
|
2022-04-18 07:31:14 +02:00 |
|
James Fellows Yates
|
6307a9cf43
|
Typos
|
2022-04-18 07:28:09 +02:00 |
|
James Fellows Yates
|
491c2d8949
|
Revert "Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages."
This reverts commit 564474cafe .
|
2022-04-18 07:26:15 +02:00 |
|
James Fellows Yates
|
564474cafe
|
Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages.
|
2022-04-18 07:21:12 +02:00 |
|