millironx/taxprofiler
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105 commits 7 branches 0 tags 7.5 MiB
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20 commits

Author SHA1 Message Date
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
James Fellows Yates
482112bb42 Start work on host removal 2022-04-03 07:58:40 +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
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
a425a322f2 refactor: make metaphlan3 run in workflow 2022-04-02 14:59:44 +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
76e9624e3f NOW commit the adapte rtrim flag 2022-03-30 11:31:37 +02:00
James Fellows Yates
4e93abc7c0 Add read improved read preprocessing 2022-03-25 14:58:06 +01:00
James Fellows Yates
cc9368ee52 Prettier linting and update schema 2022-03-24 15:35:09 +01:00
James Fellows Yates
8012998542 Make parameter naming more consistent for clipmerge 2022-03-21 19:52:50 +01:00
ljmesi
c97de32434 Make adapter and quality trimming optional 2022-03-21 18:17:08 +01:00
James A. Fellows Yates
ac77676d2b
Merge branch 'dev' into nf-core-template-merge-2.3 2022-03-17 13:11:34 +01:00
nf-core-bot
699d26b149 Template update for nf-core/tools version 2.3 2022-03-15 21:05:37 +00:00
James Fellows Yates
2c183ed2ed Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue) 2022-03-03 17:42:02 +01:00
James Fellows Yates
278f5605ca Added database preparation and final channel for profiling 2022-02-19 12:36:08 +01:00
James Fellows Yates
cf55cc592c Get skeleton read processing to input for profiling 2022-02-18 16:51:01 +01:00
James A. Fellows Yates
c68afbbf90
Update nextflow.config 2022-02-18 08:45:06 +01:00
James Fellows Yates
12e7b428f2 initial template build from nf-core/tools, version 2.2 2022-02-18 07:55:14 +01:00