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19 commits

Author SHA1 Message Date
James Fellows Yates
2d64628552 Fix left-over warns from loca modules 2023-01-20 13:33:43 +01:00
Sofia Stamouli
d691b89727 Merge branch 'dev' into nf-core-template-merge-2.7.2 2022-12-20 15:14:41 +01:00
James A. Fellows Yates
25bb4304e8
Merge pull request #187 from nf-core/revert-pep 
Revert PEP validation back to python samplesheet check
 2022-12-20 15:03:18 +01:00
nf-core-bot
ab591e01ff Template update for nf-core/tools version 2.7.2 2022-12-19 12:10:58 +00:00
James Fellows Yates
07bd989bc6 Start work on groovy native datbase checks 2022-12-12 10:02:22 +01:00
James Fellows Yates
4b68e95770 Revert PEP validation back to python samplesheet check 2022-12-12 08:49:13 +01:00
James Fellows Yates
1ccd0a0767 Merge branch 'dev' into nf-core-template-merge-2.7.1 2022-12-09 10:16:17 +01:00
nf-core-bot
36f3b5723b Template update for nf-core/tools version 2.7.1 2022-12-08 13:18:23 +00:00
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