James Fellows Yates
|
afba604e8b
|
Make everything within opt-out, once QC is opted-in
|
2022-08-30 14:04:34 +02:00 |
|
James Fellows Yates
|
95ad380173
|
Turn of length filtering by default for short read (to match opt in for longread qc)
|
2022-08-30 14:01:52 +02:00 |
|
James Fellows Yates
|
2cc07183a0
|
Standardise QC parameter system and turn on both porechop/filtlong in tests
|
2022-08-30 13:58:58 +02:00 |
|
James Fellows Yates
|
d4af88e3ff
|
Make kaiju parameter clearer for documentation purpses and update documentation
|
2022-08-25 15:50:28 +02:00 |
|
James Fellows Yates
|
d6d51e0e43
|
Start work on reordering json schema parameters
|
2022-08-24 15:23:51 +02:00 |
|
James A. Fellows Yates
|
1821496a49
|
Merge pull request #90 from nf-core/samplesheet-check-improvement
Make check_samplesheet.py compatible with nf-core/fetchngs
|
2022-08-23 15:57:59 +01:00 |
|
James A. Fellows Yates
|
22e03e73e3
|
Merge pull request #111 from nf-core/minimal-test
Add test_nothing config profile for very minimal testing
|
2022-08-23 15:57:52 +01:00 |
|
James A. Fellows Yates
|
a3055bf6da
|
Update conf/test_nothing.config
|
2022-08-23 15:48:02 +02:00 |
|
James A. Fellows Yates
|
4315141c5f
|
Update bin/check_samplesheet.py
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
|
2022-08-23 15:44:53 +02:00 |
|
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 |
|