56 commits

Author	SHA1	Message	Date
James A. Fellows Yates	6dbeb5913a	Remove left over skips	2023-03-07 13:18:58 +01:00
James A. Fellows Yates	54e8857233	Reduce number of tests to check just each tool option is tested	2023-03-07 13:06:32 +01:00
James Fellows Yates	6d9cdd3c78	And the other file	2023-03-03 09:15:21 +01:00
James A. Fellows Yates	6c2ce4a1c9	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 08:37:31 +01:00
James Fellows Yates	5c549e5ce3	Remove TODOs and references to under development	2023-03-02 13:49:03 +01:00
James Fellows Yates	2439aa69d0	Use specific samplesheet for MALT without LR reads due to GHA memory limits	2023-01-24 10:58:03 +01:00
Sofia Stamouli	d691b89727	Merge branch 'dev' into nf-core-template-merge-2.7.2	2022-12-20 15:14:41 +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	dca0b86c78	Fix versions	2022-12-09 10:28:48 +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	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
Moritz E. Beber	fdb8a7f740	Merge branch 'devel' into nf-core-template-merge-2.6	2022-10-05 12:21:54 +02:00
nf-core-bot	51bacb00e6	Template update for nf-core/tools version 2.6	2022-10-05 03:30:53 +00:00
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