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Author SHA1 Message Date
James Fellows Yates
e6c7939305 Add test_nothing config profile for minimal testing 2022-08-23 14:37:01 +02:00
James Fellows Yates
a97bb69cd2 Prettier 2022-08-23 14:24:57 +02:00
James A. Fellows Yates
de70b0a01d
Merge pull request #109 from nf-core/centrifuge_mqc 
Trying to get Centrifuge output into MQC
 2022-07-29 13:36:25 +02:00
James A. Fellows Yates
3e24f491b5
Merge pull request #106 from nf-core/porechop-log 
Add emitting porechop logs to multiqc and fix collection of others
 2022-07-29 10:58:12 +02:00
James A. Fellows Yates
f48b22d615
Apply suggestions from code review 2022-07-29 09:52:49 +02:00
James Fellows Yates
873a13e028 Merge remote-tracking branch 'origin/dev' into porechop-log 2022-07-29 09:51:34 +02:00
Mahwash Jamy
06298e867c
Merge pull request #105 from genomic-medicine-sweden/diamond-update 
Update the dev branch with the DIAMOND module update
 2022-07-28 17:21:59 +02:00
mjamy
5cdf5e958a Updated modules.config to add 'log' in diamond config 2022-07-28 16:08:15 +02:00
Mahwash Jamy
49487593e2
Merge branch 'nf-core:dev' into diamond-update 2022-07-28 15:48:59 +02:00
Sofia Stamouli
ba928af5ab
Merge pull request #110 from genomic-medicine-sweden/update_centrifuge_kreport 
Update centrifuge kreport
 2022-07-28 10:36:30 +02:00
sofstam
71cf32cc6a Add error strategy for centrifuge/kreport 2022-07-28 08:54:32 +02:00
sofstam
9bc45a3f24 Update centrifuge/kreport 2022-07-27 14:44:26 +02:00
sofstam
cecbb41f88 Update centrifuge/kreport 2022-07-27 14:42:35 +02:00
James Fellows Yates
25bcc0798d Start work on multiQC config with distinguishing Kraken/Centrifuge 2022-07-27 14:40:17 +02:00
nf-core-bot
a3bcf8665a [automated] Fix linting with Prettier 2022-07-26 18:47:40 +00:00
James A. Fellows Yates
65ae82efc4 Define separte krakena nd centrigfue modules 2022-07-26 18:37:33 +00:00
James A. Fellows Yates
9d2be68fb8 Merge branch 'dev' into centrifuge_mqc 2022-07-26 18:01:30 +00:00
James A. Fellows Yates
1ef0975736 Merge branch 'dev' into porechop-log 2022-07-26 18:00:28 +00:00
James A. Fellows Yates
fdd9a3bc4d
Merge pull request #107 from nf-core/fix-multiqc-mixing 
Fix MultiQC mixing
 2022-07-26 12:38:52 +02:00
James A. Fellows Yates
65b0af9a8b Fix profiling channels 2022-07-26 08:53:43 +00:00
James A. Fellows Yates
3054dea7c2 Get multiqc input working 2022-07-26 08:41:06 +00:00
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