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106 commits

Author SHA1 Message Date
sofstam
71cf32cc6a Add error strategy for centrifuge/kreport 2022-07-28 08:54:32 +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
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
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
069370db86
Add unclassified and verbose flags to kaiju2krona 2022-06-28 09:00:42 -05:00
18284e6e32
Add run_krona option to allow skipping Krona chart creation 2022-06-27 08:45:08 -05:00
0e8edd5b2f
Add output configuration for Kraken Krona chart 2022-06-27 08:25:47 -05:00
James Fellows Yates
9462032d00 Fix MALT save_alignemnts reads and some clean up 2022-06-03 22:29:04 +02:00
JIANHONG OU
c8a59adbce remove the database auto-download for mOTUs. 2022-06-03 14:13:58 -04:00
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
James Fellows Yates
16ec5bf74a Update parameter names 2022-05-31 20:11:19 +02:00
JIANHONG OU
f0eb88cbe2 add mOTUs to modules.config 2022-05-31 08:57:00 -04:00
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 A. Fellows Yates
d67543503b
Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-05-07 13:15:21 +02:00
James Fellows Yates
0f651873dd Linting 2022-05-07 06:12:24 +02:00
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
ljmesi
d94534e8ac Simplify params which control host removal publish 2022-05-05 09:07:33 +02:00
ljmesi
a821f748ee Add modules 2022-05-03 09:28:46 +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
a4a9b161d8 Lintin 2022-04-29 22:02:44 +02:00
James Fellows Yates
8126d16dee Add draft version of DIAMOND 2022-04-29 21:59:42 +02:00
sofstam
d082d67bcb Add kaiju2table to taxprofiler 2022-04-25 17:36:29 +02:00
Sofia Stamouli
e7e24c2d95 Prettier and suggestions from review 2022-04-25 09:21:29 +02:00
sofstam
c00ca1c2b8 Add centrifuge kreport in taxprofiler 2022-04-22 15:24:10 +02:00
James A. Fellows Yates
63230c3254
Merge pull request #63 from nf-core/maxforks
Update test.config to only allow maxFork to 1 for MALT_RUN
2022-04-21 12:57:37 +02:00
James A. Fellows Yates
cd3c8f6a89
Merge branch 'dev' into hostremoval-publish-fix 2022-04-21 11:43:06 +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
Sofia Stamouli
236141f065 Resolve conflicts with dev 2022-04-20 10:17:10 +02:00
James A. Fellows Yates
d16cd75652
Merge branch 'dev' into hostremoval-publish-fix 2022-04-20 09:53:51 +02:00
sofstam
1b7ff2265d Update usage.md, reformat test.config and modules.config 2022-04-19 13:04:58 +02:00
James Fellows Yates
9880baa0b8 Get build directory working 2022-04-18 06:37:23 +02:00
James Fellows Yates
2cfcdf2dd2 Add finer controler over for hostremoval saving 2022-04-17 22:27:04 +02:00
James Fellows Yates
cc73cdd51d Add generation of taxon-table like output for MALT 2022-04-16 07:42:30 +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