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656 commits 7 branches 0 tags 7.5 MiB
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63 commits

Author SHA1 Message Date
James A. Fellows Yates
a34b240dfc
Merge pull request #174 from nf-core/malt-update 
Update MALT
 2022-12-01 13:58:30 +01:00
James Fellows Yates
d7fbe55849 Add KU to the test profiles and add id to KU processes 2022-11-29 14:19:01 +01:00
James A. Fellows Yates
f114cc4122
Apply suggestions from code review 2022-11-24 16:55:19 +01:00
James A. Fellows Yates
17b1e3df1c
Update test.config 2022-11-24 16:53:39 +01:00
James Fellows Yates
a20b3e3c58 Try to reduce MALT memory 2022-11-24 15:51:12 +01:00
Moritz E. Beber
767663d975 chore: add Bracken to test configs 2022-10-14 12:18:55 +02:00
Rafal Stepien
5f3eee9a4a Add working version of PEP-nf-core integration 2022-09-14 14:28:48 -04:00
James A. Fellows Yates
13e9957e14 Fixes process selector warning 2022-09-02 06:03:05 +00:00
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
2cc07183a0 Standardise QC parameter system and turn on both porechop/filtlong in tests 2022-08-30 13:58:58 +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
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
Thomas A. Christensen II
18284e6e32
Add run_krona option to allow skipping Krona chart creation 2022-06-27 08:45:08 -05:00
James Fellows Yates
9462032d00 Fix MALT save_alignemnts reads and some clean up 2022-06-03 22:29:04 +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
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
JIANHONG OU
4d77b47e8d create a new test profile config for mOTUs. 2022-05-31 08:47:38 -04:00
James Fellows Yates
310ac6b450 Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong 2022-05-31 13:05:52 +02:00
JIANHONG OU
68d0cc00fa add motus profile. 2022-05-23 08:05:06 -04:00
James Fellows Yates
47a5ae0cff Add FASTP complexity option 2022-05-07 06:09:05 +02:00
James Fellows Yates
87a1d80519 Add working output for Kraken2/Centrifuge/DIAMOND 2022-05-07 05:22:35 +02:00
ljmesi
6618e8cac6 Change param to a more generic name 2022-05-05 13:20:34 +02:00
ljmesi
557d31dfd2 Add parameter for turning on longread host removal 2022-05-05 13:19:10 +02:00
James Fellows Yates
031cb45934 Add initial longread QC filtering - requires filtlong module update 2022-05-01 07:18:14 +02:00
James Fellows Yates
0630fce3b5 Tweak based on official DIAMOND test-data 2022-04-30 08:11:40 +02:00
James Fellows Yates
8126d16dee Add draft version of DIAMOND 2022-04-29 21:59:42 +02:00
James A. Fellows Yates
d850333e11
Linting 2022-04-20 13:42:26 +02:00
James A. Fellows Yates
d031322c16
Update test.config 2022-04-20 13:41:01 +02:00
sofstam
1b7ff2265d Update usage.md, reformat test.config and modules.config 2022-04-19 13:04:58 +02:00
sofstam
68ce5843a4 Add kaiju in taxprofiler 2022-04-13 18:51:56 +02:00
James A. Fellows Yates
5e80df0f94
Apply suggestions from code review 2022-04-13 15:27:53 +02:00
James Fellows Yates
aa2d07c42a Fix merge cockup 2022-04-13 14:19:19 +02:00
James A. Fellows Yates
70f94603b0
Merge branch 'dev' into hostremoval 2022-04-13 13:59:51 +02:00
James Fellows Yates
dfeaa0d1fe Rename subworkflow parameters for consistency 2022-04-13 12:00:28 +02:00
James A. Fellows Yates
025083061e
Merge branch 'dev' into hostremoval 2022-04-11 13:36:03 +02:00
Sofia Stamouli
48d28cf8d4
Update conf/test.config 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-08 10:00:10 +02:00
Sofia Stamouli
2dfe3b3cc1
Update conf/test.config 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-08 10:00:04 +02:00
sofstam
26779a4420 Remove db_name from nextflow.config 2022-04-07 16:27:19 +02:00
sofstam
606e5da7d5 Check if PR works with centrifuge/centrifuge module 2022-04-07 16:13:17 +02:00
James A. Fellows Yates
b554aa3e4d
Merge branch 'dev' into hostremoval 2022-04-07 14:00:10 +02:00
James Fellows Yates
d46ddd972c Expand tests and fix schema after review 2022-04-05 11:04:30 +02:00
James A. Fellows Yates
3d662d2e06
Merge branch 'dev' into complexity-filter-bbduk 2022-04-04 21:19:36 +02:00
sofstam
d897c922b2 Add centrifuge classificatioN 2022-04-04 13:51:51 +02:00
James A. Fellows Yates
b2e29ea23a
Merge branch 'dev' into hostremoval 2022-04-03 17:24:07 +02:00
James Fellows Yates
066ceb2bca Remove flagstat as bowtie2 reports this itself 2022-04-03 17:23:14 +02:00
James Fellows Yates
02d950c58c Fix test so complexity filter actually executes 2022-04-02 17:18:20 +02:00
James Fellows Yates
7f1a7fb4e7 Add complexity filtering to test profile 2022-04-02 17:05:54 +02:00