Moritz E. Beber
4529e7e545
refactor: change parameter exclude unmerged to include
2022-12-04 21:36:12 +01:00
James A. Fellows Yates
76a662ecc5
Fix adapterremoval adapter conflict and add optional adapter list file
2022-10-27 12:17:19 +00:00
Moritz E. Beber
f5af9fd939
fix: adjust import paths to re-organization
2022-10-05 13:40:43 +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
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 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
39e5e802c7
refactor: make code more explicit, add comment
2022-04-05 11:29:39 +02:00
Moritz E. Beber
0e9b2989e3
refactor: remove superfluous ENSURE_FASTQ_EXTENSION
2022-04-05 10:53:04 +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
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
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
James Fellows Yates
93aaa9eeac
Clean up AdapterRemoval and remove all debugging dumps
2022-04-01 21:36:22 +02:00
James A. Fellows Yates
03e832954f
Update subworkflows/local/shortread_adapterremoval.nf
...
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-04-01 20:55:33 +02:00
James A. Fellows Yates
14f2b7bd84
Apply suggestions from code review
...
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-04-01 15:34:05 +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
c4c93bd59d
Start working on adding adapterremoval
2022-03-31 15:31:45 +02:00
