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Author SHA1 Message Date
James Fellows Yates
7b08c49cd6 Re-add run merging and gonna let GHA see if it works >.> 2022-04-08 11:54:54 +02:00
Sofia Stamouli
5f24f94391
Merge pull request #31 from genomic-medicine-sweden/classification_centrifuge 
Add centrifuge classification (centrifuge/centrifuge module)
 2022-04-08 11:26:57 +02:00
Sofia Stamouli
63bc597daf Prettier 2022-04-08 11:01:45 +02:00
Sofia Stamouli
fd5ebea9a6 Remove old centrifuge module 2022-04-08 10:57:58 +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
Sofia Stamouli
3d45ac57ae Prettier 2022-04-07 16:42:22 +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 A. Fellows Yates
4c4475c316
Merge pull request #43 from nf-core/refactor-config 
Refactor config
 2022-04-06 11:03:45 +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
e72be724a6
Merge pull request #36 from nf-core/complexity-filter-bbduk 
Add bbduk and prinseq complexity (entropy or dust-based) short read filtering
 2022-04-05 16:45:40 +02:00
James Fellows Yates
82aa89ad63 re add missing switch meta of merged reads to true 2022-04-05 13:55:11 +02:00
James Fellows Yates
98f082d7b6 Fix mistake in previous upstream merge with AR2 output channel for settings file 2022-04-05 13:17:54 +02:00
James Fellows Yates
4dbd0ddc73 Merge branch 'complexity-filter-bbduk' of github.com:nf-core/taxprofiler into complexity-filter-bbduk 2022-04-05 13:14:13 +02:00
James Fellows Yates
5b9355725d Whoops 2022-04-05 13:14:06 +02:00
James A. Fellows Yates
23fb319779
Merge branch 'dev' into complexity-filter-bbduk 2022-04-05 13:11:15 +02:00
James Fellows Yates
245a4d1f5d Fix MQC staging and remove debugging dump 2022-04-05 13:08:44 +02:00
Moritz E. Beber
b37a9c5576
Merge pull request #42 from nf-core/refactor-adapterremoval 
Refactor adapterremoval
 2022-04-05 12:04:36 +02:00
Moritz E. Beber
39e5e802c7 refactor: make code more explicit, add comment 2022-04-05 11:29:39 +02:00
Moritz E. Beber
59b2088aa1 style: apply prettier 2022-04-05 11:16:43 +02:00
James Fellows Yates
d46ddd972c Expand tests and fix schema after review 2022-04-05 11:04:30 +02:00
Moritz E. Beber
0e9b2989e3 refactor: remove superfluous ENSURE_FASTQ_EXTENSION 2022-04-05 10:53:04 +02:00
Moritz E. Beber
c54c32c494 chore: update adapterremoval 2022-04-05 10:18:34 +02:00
James Fellows Yates
bb6dd738bd Merge branch 'complexity-filter-bbduk' of github.com:nf-core/taxprofiler into complexity-filter-bbduk 2022-04-04 21:21:34 +02:00
James Fellows Yates
613f6a5565 Prettier 2022-04-04 21:21:29 +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
3a56206513 Centrifuge classification 2022-04-04 16:55:48 +02:00
sofstam
d897c922b2 Add centrifuge classificatioN 2022-04-04 13:51:51 +02:00
James Fellows Yates
a76576c16b Prettier 2022-04-03 17:24:50 +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
Moritz E. Beber
fe628b3578
Merge pull request #29 from nf-core/add-metaphlan 
Add metaphlan3
 2022-04-03 09:08:01 +02:00
James Fellows Yates
482112bb42 Start work on host removal 2022-04-03 07:58:40 +02:00
James Fellows Yates
d3572e1878 Final MQC fix for AR2 (remove too-early collect) 2022-04-03 07:28:01 +02:00
Moritz E. Beber
f5baf910be
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-03 00:21:09 +02:00
Moritz E. Beber
be93eae640 fix: insert .fastq file extension 
The MetaPhlAn3 module computes the input type from the file extension
without the possibility to configure an override. Since AdapterRemoval2
creates files without `.fastq` extensions, MetaPhlAn3 input was determined
to be SAM.
 2022-04-02 21:50:13 +02:00
James Fellows Yates
02d950c58c Fix test so complexity filter actually executes 2022-04-02 17:18:20 +02:00
James Fellows Yates
469e4f3682 Remove remaining debugging .dumps( 2022-04-02 17:07:30 +02:00
James Fellows Yates
7f1a7fb4e7 Add complexity filtering to test profile 2022-04-02 17:05:54 +02:00
Moritz E. Beber
4eab257d68 style: prettify comment 2022-04-02 17:05:46 +02:00
James Fellows Yates
b055df5ea0 Add bbduk complexity (entropy-based) filtering 2022-04-02 17:02:05 +02:00
Moritz E. Beber
41526e8a64 try to fix locale 2022-04-02 15:44:39 +02:00
Moritz E. Beber
4e22bc9610 fix: force UTF-8 in different locale? 2022-04-02 15:20:36 +02:00