42 commits

Author	SHA1	Message	Date
Moritz E. Beber	4529e7e545	refactor: change parameter exclude unmerged to include	2022-12-04 21:36:12 +01:00
James Fellows Yates	0a0dffa37c	Try separating MALT	2022-12-04 12:06:33 +01:00
James A. Fellows Yates	ef1d2da179	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-12-01 12:53:34 +01:00
James Fellows Yates	bc98f5b80f	Separate KrakenUniq test run	2022-12-01 10:37:14 +01:00
Moritz E. Beber	6b538d658a	chore: let all tests run to completion	2022-11-22 10:13:10 +01:00
Sofia Stamouli	8c3e80b6ea	Add helptest to nextflow_schema,add versions to longread_preprocessing	2022-10-25 11:13:26 +02:00
Sofia Stamouli	511cb16a61	Apply review suggestions	2022-10-20 16:55:57 +02:00
Sofia Stamouli	8eddb32b88	Add Falco as an alternative to FastQC	2022-10-18 17:43:16 +02:00
James A. Fellows Yates	dd194f3f47	Fix mOTUs CI and old param warn	2022-09-04 15:01:58 +00:00
James A. Fellows Yates	331231ea28	Standardise CI execution	2022-09-04 14:02:54 +00:00
James Fellows Yates	c3427e44b3	Try with retries from sarek approach	2022-09-02 12:24:29 +02:00
James Fellows Yates	7917e1d656	Synronise mOTUs CI setup	2022-09-02 11:51:18 +02:00
James Fellows Yates	55d7919fa7	Revert "Update ci.yml" ... This reverts commit 176a0a6280.	2022-09-02 11:48:57 +02:00
James Fellows Yates	c479714a5e	Revert "Update ci.yml" ... This reverts commit 61560cf065.	2022-09-02 11:48:49 +02:00
James A. Fellows Yates	61560cf065	Update ci.yml	2022-09-02 10:12:27 +02:00
James A. Fellows Yates	176a0a6280	Update ci.yml	2022-09-02 10:06:20 +02:00
James A. Fellows Yates	28d8d3f8fb	Merge branch 'dev' into nf-core-template-merge-2.5	2022-08-31 09:16:34 +02:00
nf-core-bot	6dfca81761	Template update for nf-core/tools version 2.5	2022-08-30 13:43:03 +00:00
JIANHONG OU	713a341e09	clean up ci.yml	2022-06-03 15:22:33 -04:00
JIANHONG OU	9fa6ecad56	debug for database csv file	2022-06-03 14:50:03 -04:00
JIANHONG OU	3cd3d2dad3	prettier write .	2022-06-03 14:38:59 -04:00
JIANHONG OU	22f65eedc7	fix the download address for downloadDB for mOTUs.	2022-06-03 14:16:25 -04:00
JIANHONG OU	c8a59adbce	remove the database auto-download for mOTUs.	2022-06-03 14:13:58 -04:00
James A. Fellows Yates	53c4399052	Merge branch 'dev' into motus	2022-06-02 21:38:35 +02:00
JIANHONG OU	4d77b47e8d	create a new test profile config for mOTUs.	2022-05-31 08:47:38 -04:00
James Fellows Yates	310ac6b450	Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong	2022-05-31 13:05:52 +02:00
Moritz E. Beber	a9fbe47992	Merge branch 'dev' into nf-core-template-merge-2.4	2022-05-19 08:42:28 +02:00
nf-core-bot	a560492353	Template update for nf-core/tools version 2.4	2022-05-16 10:22:38 +00:00
James Fellows Yates	3fa2181f49	Fix prinseq tool selection	2022-05-07 06:15:15 +02:00
James Fellows Yates	031cb45934	Add initial longread QC filtering - requires filtlong module update	2022-05-01 07:18:14 +02:00
James Fellows Yates	aa2d07c42a	Fix merge cockup	2022-04-13 14:19:19 +02:00
James A. Fellows Yates	70f94603b0	Merge branch 'dev' into hostremoval	2022-04-13 13:59:51 +02:00
James Fellows Yates	dfeaa0d1fe	Rename subworkflow parameters for consistency	2022-04-13 12:00:28 +02:00
James Fellows Yates	29073e3c93	Update CI tests	2022-04-11 13:38:42 +02:00
James Fellows Yates	d130a72d74	Get this working	2022-04-08 13:09:23 +02:00
James Fellows Yates	7b08c49cd6	Re-add run merging and gonna let GHA see if it works >.>	2022-04-08 11:54:54 +02:00
James Fellows Yates	d46ddd972c	Expand tests and fix schema after review	2022-04-05 11:04:30 +02:00
Moritz E. Beber	41526e8a64	try to fix locale	2022-04-02 15:44:39 +02:00
James Fellows Yates	0d0b377dfb	Add additional test	2022-04-01 11:19:00 +02:00
nf-core-bot	6b939e6728	Template update for nf-core/tools version 2.3.1	2022-03-23 13:57:56 +00:00
nf-core-bot	699d26b149	Template update for nf-core/tools version 2.3	2022-03-15 21:05:37 +00:00
James Fellows Yates	12e7b428f2	initial template build from nf-core/tools, version 2.2	2022-02-18 07:55:14 +01:00