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

Author SHA1 Message Date
James A. Fellows Yates
e6e8ed7cc9 Add some debugging notes 2022-03-26 20:54:50 +00:00
James Fellows Yates
120382f51d Fix input channels to kraken2 2022-03-26 06:45:16 +01:00
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 A. Fellows Yates
edce6603ef
Merge branch 'dev' into nf-core-template-merge-2.3.2 2022-03-24 14:10:58 +01:00
nf-core-bot
6b939e6728 Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00
James Fellows Yates
81bfb629ca Add working basic test to begin 2022-03-21 20:28:09 +01:00
James Fellows Yates
8012998542 Make parameter naming more consistent for clipmerge 2022-03-21 19:52:50 +01:00
ljmesi
f6fe26de46 Rename shortread subworkflow to be more consistent 2022-03-21 18:25:56 +01:00
ljmesi
c97de32434 Make adapter and quality trimming optional 2022-03-21 18:17:08 +01:00
ljmesi
582aaa105f Include long reads preprocessing subworkflow 2022-03-18 15:12:07 +01:00
Lauri Mesilaakso
0936b9b28e
Update workflows/taxprofiler.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-03-18 14:18:38 +01:00
ljmesi
c8e49c56f4 Perform fastqc on nanopore reads before trimming 2022-03-18 13:47:44 +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
e39c6a8ccb Fix MALT multiqc report clash 2022-03-03 18:04:03 +01:00
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 Fellows Yates
12e7b428f2 initial template build from nf-core/tools, version 2.2 2022-02-18 07:55:14 +01:00