millironx/taxprofiler
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281 commits 7 branches 0 tags 7.5 MiB
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65 commits

Author SHA1 Message Date
James Fellows Yates
16ec5bf74a Update parameter names 2022-05-31 20:11:19 +02:00
James Fellows Yates
310ac6b450 Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong 2022-05-31 13:05:52 +02:00
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
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
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
cd3c8f6a89
Merge branch 'dev' into hostremoval-publish-fix 2022-04-21 11:43:06 +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
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
967b1f7d6e
Merge branch 'dev' into run-merging 2022-04-12 09:28:10 +02:00
James Fellows Yates
a5f4fc42d5 Fix run merging for unmerged PE data 2022-04-12 09:25:27 +02:00
James A. Fellows Yates
025083061e
Merge branch 'dev' into hostremoval 2022-04-11 13:36:03 +02:00
James Fellows Yates
082093f3de Prettier 2022-04-10 06:44:10 +02:00
James Fellows Yates
ecf0eea4f9 Move profiling to subworkflow and standardise outputs 2022-04-10 06:43:30 +02:00
James Fellows Yates
ca011ccc5b Fix cat_fastq naming logic? 2022-04-08 13:28:37 +02:00
James Fellows Yates
d130a72d74 Get this working 2022-04-08 13:09:23 +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
Moritz E. Beber
7ab3aa546b refactor: use flags to publish reads 2022-04-06 10:27:11 +02:00
Moritz E. Beber
018b9a8ea6 refactor: do not generally publish output 2022-04-06 10:21:43 +02:00
Moritz E. Beber
8827b143a2 fix: disable publishing correctly 2022-04-05 20:56:19 +02:00
Moritz E. Beber
af12435fa5 fix: use parameter for publish mode everywhere 2022-04-05 20:56:19 +02:00
Moritz E. Beber
c40a9a0011 refactor: avoid publishing unpacked databases 2022-04-05 20:54:32 +02:00
James A. Fellows Yates
3d662d2e06
Merge branch 'dev' into complexity-filter-bbduk 2022-04-04 21:19:36 +02:00
James Fellows Yates
a384162810 Add prinseq as alternative complexity filtering 2022-04-04 21:16:51 +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
b055df5ea0 Add bbduk complexity (entropy-based) filtering 2022-04-02 17:02:05 +02:00
Moritz E. Beber
70862570e0 fix: use same naming scheme 2022-04-02 15:00:26 +02:00
Moritz E. Beber
b0b5936fe8 chore: configure output for metaphlan3 2022-04-02 15:00:26 +02:00
James Fellows Yates
dcda815bfb Add final adapterremoval options to match fastp functionality 2022-04-01 09:50:08 +02:00
James Fellows Yates
76e9624e3f NOW commit the adapte rtrim flag 2022-03-30 11:31:37 +02:00
James Fellows Yates
231253227c Remove run merging for now due to complexity 2022-03-28 16:38:10 +02:00
James Fellows Yates
8dc9e583ad Debugging run merging 2022-03-27 09:30:23 +02:00
James A. Fellows Yates
e6e8ed7cc9 Add some debugging notes 2022-03-26 20:54:50 +00:00