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Author SHA1 Message Date
Moritz E. Beber
fe628b3578
Merge pull request #29 from nf-core/add-metaphlan 
Add metaphlan3
 2022-04-03 09:08:01 +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
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
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
James Fellows Yates
ee53283696 Debugging comment 2022-03-28 09:13:05 +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
James A. Fellows Yates
622fafedc8 Prempt centrifuge database untar crash 2022-03-26 20:22:35 +00:00
James Fellows Yates
120382f51d Fix input channels to kraken2 2022-03-26 06:45:16 +01:00
James A. Fellows Yates
000f129dab
Apply suggestions from code review 2022-03-25 15:32:56 +01:00
James Fellows Yates
ede362dbf9 Remove duplicate config and sync longread fastqc 2022-03-25 15:28:30 +01:00
James Fellows Yates
b763bfa2c0 More cleanup 2022-03-25 15:26:57 +01:00
James Fellows Yates
0e6f7e2ca1 Revert "Some more cleanup" 
This reverts commit 7ddcb09a85.
 2022-03-25 15:24:10 +01:00
James Fellows Yates
7ddcb09a85 Some more cleanup 2022-03-25 15:22:41 +01:00
James Fellows Yates
b5f5c75504 Fix file header descriptions 2022-03-25 15:21:52 +01:00
James Fellows Yates
dfcf8f7b1a Prettier 2022-03-25 15:10:52 +01:00
James Fellows Yates
ff1f28f4f0 Update schema 2022-03-25 15:01:25 +01:00
James Fellows Yates
4e93abc7c0 Add read improved read preprocessing 2022-03-25 14:58:06 +01:00
James A. Fellows Yates
fafb7e0f6f
Update README.md 2022-03-24 16:59:12 +01:00
James A. Fellows Yates
f3c21203c8
Merge pull request #32 from nf-core/nf-core-template-merge-2.3.2 
Important! Template update for nf-core/tools v2.3.2
 2022-03-24 15:50:38 +01:00