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Author SHA1 Message Date
James Fellows Yates
02c06b9f7b Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file 2022-06-30 18:33:11 +02:00
James Fellows Yates
27f174d17e Merge remote-tracking branch 'origin/dev' into malt-to-krona 2022-06-30 12:01:33 +02:00
James Fellows Yates
0050f45345 Add taxonomy directory param 2022-06-30 11:43:52 +02:00
James A. Fellows Yates
913080a5b1
Merge pull request #96 from MillironX/feature/kaiju2krona 
Add Krona output for Kaiju profiles
 2022-06-29 09:27:25 +02:00
Thomas A. Christensen II
6673ccf8d8
Update channel assignment alignment in profiling subworkflow 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-28 09:00:43 -05:00
Thomas A. Christensen II
069370db86
Add unclassified and verbose flags to kaiju2krona 2022-06-28 09:00:42 -05:00
Thomas A. Christensen II
4de43040a3
Switch to using raw classifications for Kaiju2Krona 2022-06-28 09:00:41 -05:00
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
821dd844d8
Add Kaiju profile conversion to visualization workflow 2022-06-27 09:23:20 -05:00
Thomas A. Christensen II
5b80c7cab9
Install KAIJU_KAIJU2KRONA 2022-06-27 08:58:28 -05:00
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
James A. Fellows Yates
2e7f26f380 Replace header tuple with sub-set list of only relevant columns for sample checking 2022-06-14 20:09:48 +00:00
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 Fellows Yates
c1a7d6335f Do not require fixed column order 2022-06-13 21:02:12 +02:00
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
dc48935651
Apply suggestions from code review 2022-06-07 20:19:45 +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
JIANHONG OU
713a341e09 clean up ci.yml 2022-06-03 15:22:33 -04:00
JIANHONG OU
9fa6ecad56 debug for database csv file 2022-06-03 14:50:03 -04:00
JIANHONG OU
3cd3d2dad3 prettier write . 2022-06-03 14:38:59 -04:00
JIANHONG OU
22f65eedc7 fix the download address for downloadDB for mOTUs. 2022-06-03 14:16:25 -04:00
JIANHONG OU
c8a59adbce remove the database auto-download for mOTUs. 2022-06-03 14:13:58 -04:00
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
53c4399052
Merge branch 'dev' into motus 2022-06-02 21:38:35 +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