11 commits

Author	SHA1	Message	Date
Moritz E. Beber	563b34c9c3	refactor: rename process to kraken2	2022-10-14 14:48:27 +02:00
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
Thomas A. Christensen II	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