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Author SHA1 Message Date
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
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 
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
James Fellows Yates
98dc8014a5 Fix kraken2 module 2022-03-28 16:46:45 +02:00
James Fellows Yates
231253227c Remove run merging for now due to complexity 2022-03-28 16:38:10 +02:00
sofstam
0e0e8128e8 Prettier format 2022-03-28 13:53:16 +02:00
James Fellows Yates
ee53283696 Debugging comment 2022-03-28 09:13:05 +02:00