Moritz E. Beber
7f8180f458
fix: emit tool versions
2022-10-14 12:49:07 +02:00
Moritz E. Beber
ca38d002de
feat: integrate Bracken into the profiling pipeline
2022-10-14 12:18:07 +02:00
Moritz E. Beber
4f728648f5
feat: add process to standardize kraken report
2022-10-14 10:56:14 +02:00
James Fellows Yates
43a8aa4405
Remove detect_reads.py and replace remaining checks with nextflow code instead
2022-09-27 15:32:51 +02:00
Rafal Stepien
e84b64f7e1
Update modules/local/samplesheet_check.nf
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-19 09:49:20 -04:00
Rafal Stepien
5f3eee9a4a
Add working version of PEP-nf-core integration
2022-09-14 14:28:48 -04:00
87678c127b
Add KRONA_CLEANUP process module
2022-06-14 10:34:33 -05:00
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
278f5605ca
Added database preparation and final channel for profiling
2022-02-19 12:36:08 +01:00
James Fellows Yates
12e7b428f2
initial template build from nf-core/tools, version 2.2
2022-02-18 07:55:14 +01:00