millironx/taxprofiler
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387 commits 7 branches 0 tags 7.5 MiB
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72 commits

Author SHA1 Message Date
James Fellows Yates
a384162810 Add prinseq as alternative complexity filtering 2022-04-04 21:16:51 +02:00
sofstam
d897c922b2 Add centrifuge classificatioN 2022-04-04 13:51:51 +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
James Fellows Yates
482112bb42 Start work on host removal 2022-04-03 07:58:40 +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
b055df5ea0 Add bbduk complexity (entropy-based) filtering 2022-04-02 17:02:05 +02:00
Moritz E. Beber
4d2960c06f chore: add metaphlan3 module 2022-04-02 14:59:44 +02:00
James Fellows Yates
c4c93bd59d Start working on adding adapterremoval 2022-03-31 15:31:45 +02:00
sofstam
37a70dc3e3 Merge branch 'dev' into classification_centrifuge 2022-03-25 16:18:35 +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
sofstam
3ff54e620e Add centrifuge classification 2022-03-24 13:02:25 +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 A. Fellows Yates
3079f16861
Merge branch 'dev' into database-untar 2022-03-21 19:55:36 +01:00
James A. Fellows Yates
631c115e10 Adds PoC of untarring system 2022-03-21 14:58:19 +00:00
James Fellows Yates
c7f022008c Start getting database prep ready 2022-03-21 15:07:59 +01:00
ljmesi
16be676d72 Add Porechop module 2022-03-18 14:34:10 +01:00
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