37 commits

Author	SHA1	Message	Date
James A. Fellows Yates	2140928638	Merge pull request #272 from nf-core/final-reads-saving ... Add 'final reads for profiling' saving mechanism	2023-04-21 15:21:35 +02:00
James A. Fellows Yates	03c3169f10	Replace all instance of exit 1 with error for safety and consistency	2023-04-04 09:41:22 +00:00
James Fellows Yates	3b90064ba4	Start adding conditions in modules.conf - non-cat not working	2023-03-22 15:39:45 +01:00
James Fellows Yates	74bc6b7dd3	Logical ordering and improved commenting	2023-03-17 22:38:05 +01:00
James Fellows Yates	68d131af34	Remove leftover dump	2023-03-17 22:30:43 +01:00
James Fellows Yates	f9af0040bf	Add multi-run meta information	2023-03-17 22:30:29 +01:00
Moritz E. Beber	bb7323e25d	fix: restore setting id on FASTQ meta	2023-03-11 11:34:47 +01:00
Moritz E. Beber	fa1c779536	fix: insert id key again	2023-03-11 11:28:42 +01:00
Moritz E. Beber	d17dce5590	style: use subMap and early returns	2023-03-11 11:28:42 +01:00
Moritz E. Beber	0bcea6c993	style: use parameter for branch closure	2023-03-11 11:28:42 +01:00
James Fellows Yates	577da7e835	Remove .first() as the module only executes once anyway and we get a ugly warning	2022-12-20 13:59:14 +01:00
James Fellows Yates	11db981a88	minor fixes	2022-12-20 13:55:15 +01:00
James A. Fellows Yates	7709245874	Update subworkflows/local/input_check.nf ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-12-20 13:54:05 +01:00
James Fellows Yates	4b68e95770	Revert PEP validation back to python samplesheet check	2022-12-12 08:49:13 +01:00
Moritz E. Beber	f5af9fd939	fix: adjust import paths to re-organization	2022-10-05 13:40:43 +02:00
James Fellows Yates	87edc4569c	Move to a function	2022-09-27 15:46:17 +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	1584d6fc51	Update workflows/taxprofiler.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-19 10:43:04 -04:00
Rafal Stepien	768f9980d8	Add pep_input_base_dir to workflow. Just need to update modules	2022-09-15 12:31:49 -04:00
Rafal Stepien	5f3eee9a4a	Add working version of PEP-nf-core integration	2022-09-14 14:28:48 -04:00
James A. Fellows Yates	ecaff371aa	Update input_check.nf	2022-04-18 07:35:19 +02:00
James Fellows Yates	491c2d8949	Revert "Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages." ... This reverts commit 564474cafe.	2022-04-18 07:26:15 +02:00
James Fellows Yates	564474cafe	Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages.	2022-04-18 07:21:12 +02:00
sofstam	d897c922b2	Add centrifuge classificatioN	2022-04-04 13:51:51 +02:00
Moritz E. Beber	a425a322f2	refactor: make metaphlan3 run in workflow	2022-04-02 14:59:44 +02:00
James Fellows Yates	93aaa9eeac	Clean up AdapterRemoval and remove all debugging dumps	2022-04-01 21:36:22 +02:00
sofstam	3ff54e620e	Add centrifuge classification	2022-03-24 13:02:25 +01:00
James Fellows Yates	81bfb629ca	Add working basic test to begin	2022-03-21 20:28:09 +01:00
James A. Fellows Yates	3079f16861	Merge branch 'dev' into database-untar	2022-03-21 19:55:36 +01:00
James Fellows Yates	c7f022008c	Start getting database prep ready	2022-03-21 15:07:59 +01:00
ljmesi	41b3d8db82	Add nanopore channel	2022-03-18 10:47:41 +01:00
ljmesi	0f0ed6cd46	Fix function name	2022-03-18 10:45:06 +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	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