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Author SHA1 Message Date
James A. Fellows Yates
e76b299705 Start working getting kraken and centrifuge working in MQC 2022-07-26 08:18:54 +00:00
James Fellows Yates
139cf0d6aa Fix 2022-07-26 10:12:33 +02:00
James A. Fellows Yates
64f01fcfe0
Merge branch 'dev' into porechop-log 2022-07-20 14:05:23 +02:00
Sofia Stamouli
1fe9c133f1
Merge pull request #103 from genomic-medicine-sweden/update_filtlong 
Update the dev branch with the filtlong update
 2022-07-20 10:44:52 +02:00
James Fellows Yates
255afee4c7 Re-add the collects 2022-07-19 17:10:10 +02:00
Mahwash Jamy
811ded38af
Update subworkflows/local/profiling.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-07-19 16:44:48 +02:00
Sofia Stamouli
237e9aa623
Update longread_preprocessing.nf 2022-07-19 16:44:08 +02:00
James A. Fellows Yates
8d7ddb5847
Apply suggestions from code review 2022-07-19 16:30:13 +02:00
mjamy
c4c82212e1 incorporate diamond log file into multiqc channel 2022-07-19 14:12:16 +02:00
sofstam
171258d545 Fix typos 2022-07-19 14:07:13 +02:00
sofstam
25bc01f9c4 Fix typos 2022-07-19 14:04:49 +02:00
sofstam
8147dba0b4 Fix typos 2022-07-19 14:03:10 +02:00
sofstam
526ed79763 Fix filtlong logs 2022-07-19 14:01:11 +02:00
sofstam
1ba6a08135 Seperate multiqc for filtlong 2022-07-19 13:53:29 +02:00
James Fellows Yates
33a5402b25 Add emitting porechop logs to multiqc and fix collection of others 2022-07-19 13:50:39 +02:00
sofstam
3f5fa8cc7a Merge branch 'dev' into update_filtlong 2022-07-19 13:50:28 +02:00
James A. Fellows Yates
6f269a8245
Merge pull request #101 from nf-core/motus/merge 
Add motus/merge and biom support
 2022-07-19 13:41:51 +02:00
mjamy
035b4b7a17 Update the dev branch with the DIAMOND module update 2022-07-15 16:28:07 +02:00
sofstam
5a2fd260fd Log file into multiqc channel 2022-07-15 12:50:50 +02:00
James Fellows Yates
d83c747533 Fix modules JSON 2022-07-15 12:38:20 +02:00
James A. Fellows Yates
c215ed5607
Merge branch 'dev' into motus/merge 2022-07-15 10:52:42 +02:00
James A. Fellows Yates
cc3967a3fd
Apply suggestions from code review 2022-07-15 10:51:41 +02:00
sofstam
6b00360ff5 Merge branch 'dev' into update_filtlong 2022-07-15 10:05:43 +02:00
James A. Fellows Yates
d7ca3df160
Merge pull request #104 from nf-core/motus-profile-update 
Update mOTUs profile module and mix log for multiqc
 2022-07-14 16:03:01 +02:00
James Fellows Yates
449b6a5553 Fix file name output clashing wiht multiqc 2022-07-13 15:25:58 +02:00
James Fellows Yates
31119f83c2 Send to MQC only the log file not the meta 2022-07-13 14:29:47 +02:00
James Fellows Yates
13280e2468 Fix .empty 2022-07-13 12:44:44 +02:00
James Fellows Yates
eaa69b65d8 Update mOTUs profile module and mix log for multiqc 2022-07-13 12:38:30 +02:00
James Fellows Yates
c22946cfab Fix motu versions not being exported if not run 2022-07-13 12:36:29 +02:00
sofstam
1fbe241d27 Update filtlong module 2022-07-12 17:43:52 +02:00
sofstam
4a316df209 Update the dev branch with the filtlong update 2022-07-12 17:15:36 +02:00
James Fellows Yates
d8c0e9e7fe Prettier 2022-07-12 11:41:07 +02:00
James Fellows Yates
a0ee82bf43 Add motus/merge and biom support 2022-07-12 11:39:26 +02:00
James A. Fellows Yates
8082c7d108
Merge pull request #97 from nf-core/malt-to-krona 
Add Krona support for MALT
 2022-07-05 15:17:52 +02:00
James A. Fellows Yates
1eba859bf8
Merge pull request #82 from jianhong/motus 
add motus profile.
 2022-07-04 14:16:12 +02:00
James A. Fellows Yates
26e31c782d
Merge branch 'dev' into motus 2022-07-04 13:14:42 +02:00
James Fellows Yates
447b8f0905 Get fixed Krona module and add Krona taxonomy to test profile 2022-07-01 17:21:19 +02:00
James Fellows Yates
97e6cdf4b4 Add Krona taxonomy DB to schema build 2022-06-30 18:36:13 +02:00
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