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
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
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
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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
Moritz E. Beber
562fa42696
fix: remove duplicate porechop entry
2022-04-02 15:00:55 +02:00
Moritz E. Beber
70862570e0
fix: use same naming scheme
2022-04-02 15:00:26 +02:00
Moritz E. Beber
817678d870
chore: add metaphlan3 run to test profile
2022-04-02 15:00:26 +02:00
Moritz E. Beber
996b3f4912
fix: correct the input shape to metaphlan3
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
Moritz E. Beber
95ed86516b
chore: add citation
2022-04-02 15:00:26 +02:00
Moritz E. Beber
e579f9f5f3
style: apply prettier
2022-04-02 14:59:44 +02:00
Moritz E. Beber
fb9afa013a
fix: add metaphlan parameter to schema
2022-04-02 14:59:44 +02:00
Moritz E. Beber
a425a322f2
refactor: make metaphlan3 run in workflow
2022-04-02 14:59:44 +02:00
Moritz E. Beber
69db920610
feat: include metaphlan3 in workflow
2022-04-02 14:59:44 +02:00
Moritz E. Beber
4d2960c06f
chore: add metaphlan3 module
2022-04-02 14:59:44 +02:00
James A. Fellows Yates
1dfbcacf68
Merge pull request #34 from nf-core/adapterremoval
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Add AdapterRemoval as alternative trimer/merger
2022-04-02 10:33:45 +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
0d0b377dfb
Add additional test
2022-04-01 11:19:00 +02:00
James Fellows Yates
df4f13319f
More linting
2022-04-01 11:13:57 +02:00
James Fellows Yates
b04cfec2c2
Prettier linting
2022-04-01 11:13:36 +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
James A. Fellows Yates
323883bd3e
Merge pull request #33 from nf-core/improve-shortread-input
...
Improve shortread input preprocessing
2022-03-30 11:48:32 +02:00
James Fellows Yates
76e9624e3f
NOW commit the adapte rtrim flag
2022-03-30 11:31:37 +02:00
James Fellows Yates
98a9688329
Change CPUs back to template, update skiptrim fiag
2022-03-29 15:18:06 +02:00
Sofia Stamouli
c552819c72
Apply prettier again
2022-03-28 22:15:31 +02:00
sofstam
d25f97c506
Prettier format
2022-03-28 22:08:05 +02:00
James Fellows Yates
04fb6f4127
Use new resources for test data
2022-03-28 20:38:16 +02:00
James Fellows Yates
94e5cfef4a
Filter long reads for MALT, bump cpus for FastQC for minigut to pass
2022-03-28 18:20:10 +02:00
James Fellows Yates
eada201eb2
Prettier
2022-03-28 16:47:37 +02:00