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Author SHA1 Message Date
James Fellows Yates
0050f45345 Add taxonomy directory param 2022-06-30 11:43:52 +02:00
James Fellows Yates
af854f5f34 Update mimetype for database csv as per https://github.com/nf-core/mag/pull/325/files 2022-06-28 12:42:41 +02:00
James A. Fellows Yates
e66c2b9b87
Merge pull request #94 from MillironX/feature/centrifuge2krona 
Add Krona output for Centrifuge profiles
 2022-06-27 17:13:31 +02:00
James A. Fellows Yates
5e554a3a0b
Merge pull request #91 from MillironX/feature/kreport2krona 
Add Krona output for Kraken classification
 2022-06-27 16:55:55 +02:00
Thomas A. Christensen II
23fec89b06
Add Krona chart creation for Centrifuge reports 2022-06-27 08:52:29 -05:00
Thomas A. Christensen II
18284e6e32
Add run_krona option to allow skipping Krona chart creation 2022-06-27 08:45:08 -05:00
Thomas A. Christensen II
15ac8b39fa
Add citation for Krona 2022-06-27 08:25:48 -05:00
Thomas A. Christensen II
0e8edd5b2f
Add output configuration for Kraken Krona chart 2022-06-27 08:25:47 -05:00
Thomas A. Christensen II
ad9bc4b7e9
Add the visualization workflow to the main workflow 2022-06-27 08:25:38 -05:00
Thomas A. Christensen II
a40a442178
Create VISUALIZATION_KRONA workflow to create Krona charts 2022-06-27 08:22:47 -05:00
James A. Fellows Yates
a83f53f64c
Merge pull request #93 from nf-core/malt-rollback 
MALT version rollback
 2022-06-20 09:43:09 +02:00
James Fellows Yates
4552b53e75 Add note about MALT version to docs 2022-06-20 08:30:23 +02:00
James Fellows Yates
4ff2145e44 Roll back MALT version 2022-06-20 08:23:14 +02:00
Thomas A. Christensen II
5da8d5b741
Install KRONA_KTIMPORTTEXT 2022-06-14 10:34:34 -05:00
Thomas A. Christensen II
87678c127b
Add KRONA_CLEANUP process module 2022-06-14 10:34:33 -05:00
Thomas A. Christensen II
a84f693479
Install KRAKENTOOLS_KREPORT2KRONA module 2022-06-14 08:13:36 -05:00
James A. Fellows Yates
3dcda7446b
Merge pull request #86 from nf-core/support-aligned-reads 
Add working read alignment output for MALT/Kraken2/Centrifuge/DIAMOND
 2022-06-13 11:23:34 +02:00
James Fellows Yates
e0ad49ebc9 Fix metadata manipulaton for malt 2022-06-10 19:33:37 +02:00
James A. Fellows Yates
621b6a3d09
Add comments about MALT id replacement and refactor for simplicity 2022-06-10 11:27:51 +02:00
James Fellows Yates
6c6f5e0913 Merge branch 'dev' of github.com:nf-core/taxprofiler into dev 2022-06-09 08:21:51 +02:00
James Fellows Yates
ec13b8d608 Remove support for uncompressed FASTQ files 2022-06-09 08:21:48 +02:00
James Fellows Yates
800c0dd2aa Merge branch 'support-aligned-reads' of github.com:nf-core/taxprofiler into support-aligned-reads 2022-06-09 08:16:01 +02:00
James Fellows Yates
490a8a8a84 Remove dump 2022-06-09 08:15:58 +02:00
James A. Fellows Yates
ebdd5683b2
Apply suggestions from code review 2022-06-03 22:33:48 +02:00
James Fellows Yates
9462032d00 Fix MALT save_alignemnts reads and some clean up 2022-06-03 22:29:04 +02:00
James Fellows Yates
d48b3be5a7 Tweak DIAMOND save_reads message 2022-06-03 13:55:17 +02:00
James Fellows Yates
3313b90453 Fix JSOn schema 2022-06-03 13:50:48 +02:00
James A. Fellows Yates
96fecb2bfc
Merge branch 'dev' into support-aligned-reads 2022-06-03 13:48:54 +02:00
James A. Fellows Yates
43ea8d299c
Merge pull request #74 from nf-core/add-filtlong 
Add initial longread QC filtering - requires filtlong module update
 2022-06-02 20:10:46 +02:00
James Fellows Yates
2838c136bd Prettier 2022-06-02 12:51:39 +02:00
James A. Fellows Yates
c9581b1796
Merge branch 'dev' into support-aligned-reads 2022-06-02 12:45:29 +02:00
James Fellows Yates
d3d28da1b1 Update after review 2022-06-02 11:53:53 +02:00
James A. Fellows Yates
a196e0f628
Merge branch 'dev' into add-filtlong 2022-06-02 11:51:26 +02:00
James A. Fellows Yates
dfcaaae1fb
Merge pull request #83 from ZandraFagernas/dev 
Uploaded logo
 2022-06-02 11:31:32 +02:00
James Fellows Yates
fa70a413cb Use finally working filtlong module 2022-05-31 21:12:09 +02:00
James Fellows Yates
16ec5bf74a Update parameter names 2022-05-31 20:11:19 +02:00
James Fellows Yates
792e2d019b Fix merge error in schema 2022-05-31 13:06:48 +02:00
James Fellows Yates
310ac6b450 Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong 2022-05-31 13:05:52 +02:00
James Fellows Yates
77da358e87 Separate dark and light mode logos, add to README and add to MQC report 2022-05-31 12:45:38 +02:00
ZandraFagernas
74b48f0919
Add files via upload 2022-05-28 13:29:24 +02:00
James A. Fellows Yates
ba75685550
Merge pull request #81 from nf-core/nf-core-template-merge-2.4 
Important! Template update for nf-core/tools v2.4
 2022-05-19 11:00:48 +01:00
Moritz E. Beber
a9fbe47992
Merge branch 'dev' into nf-core-template-merge-2.4 2022-05-19 08:42:28 +02:00
nf-core-bot
a560492353 Template update for nf-core/tools version 2.4 2022-05-16 10:22:38 +00:00
James A. Fellows Yates
63d9cbbdfd
Merge pull request #80 from nf-core/activate-pipeline-specific-profiles 
Activate institutional specific profiles
 2022-05-12 11:00:49 +02:00
James A. Fellows Yates
aca7bc439d
Update nextflow.config 2022-05-12 08:08:14 +01:00
James A. Fellows Yates
fd71b71929
Merge pull request #79 from nf-core/fastp-complexity 
Add FASTP complexity option
 2022-05-07 14:05:32 +02:00
James A. Fellows Yates
d67543503b
Apply suggestions from code review 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-05-07 13:15:21 +02:00
James Fellows Yates
3fa2181f49 Fix prinseq tool selection 2022-05-07 06:15:15 +02:00
James Fellows Yates
0f651873dd Linting 2022-05-07 06:12:24 +02:00
James Fellows Yates
47a5ae0cff Add FASTP complexity option 2022-05-07 06:09:05 +02:00