33 commits

Author	SHA1	Message	Date
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 A. Fellows Yates	5e400c8c89	Apply suggestions from code review	2023-03-11 20:06:59 +01:00
Moritz E. Beber	b90433f3c2	style: use parameters for filter closure	2023-03-11 11:28:42 +01:00
Moritz E. Beber	aa2410a871	style: use named parameters for closure	2023-03-11 11:28:42 +01:00
Moritz E. Beber	c2ad421051	refactor: simplify DB validation	2023-03-11 11:28:42 +01:00
James Fellows Yates	98bc6910d5	Update authors and remove left over comment	2023-03-07 11:47:54 +01:00
James Fellows Yates	b3837cce5b	Relax strictness so can supply empty db_params but block if only single parameter with out ;	2023-02-08 15:44:37 +01:00
James Fellows Yates	fe3d42ffd7	Make bracken db_params be a semi-colon separate list to allow kraken and bracken parameters	2023-02-08 13:34:36 +01:00
James Fellows Yates	18886c0cbc	Start trying a different method with maps in profiling	2023-02-07 15:51:25 +01:00
James A. Fellows Yates	c765b3f0bc	Merge branch 'dev' into allow-targz-motus	2023-01-24 15:20:29 +01:00
James Fellows Yates	14826d5205	Separate conditions, remove some left-over dumps	2023-01-24 13:20:58 +01:00
James A. Fellows Yates	6eafcc6499	Try Moritz's trick, assuming validate_db_rows already checks for tool name validity	2023-01-24 12:43:34 +01:00
James Fellows Yates	1a148c5d49	Remove double If and format for readability	2023-01-24 10:48:23 +01:00
James A. Fellows Yates	d56e3133f9	Allow databases of all tools to arrive as tar.gz	2023-01-24 10:45:01 +01:00
Sofia Stamouli	41c1ae9d1a	Commit suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-23 12:20:37 +01:00
sofstam	85906ab1cb	Optional untar on dbs	2022-12-23 11:25:57 +01:00
James Fellows Yates	7c66968fef	More comments	2022-12-12 11:04:21 +01:00
James Fellows Yates	460f3ca157	Add database sheet validation	2022-12-12 11:03:40 +01:00
James Fellows Yates	07bd989bc6	Start work on groovy native datbase checks	2022-12-12 10:02:22 +01:00
Moritz E. Beber	f5af9fd939	fix: adjust import paths to re-organization	2022-10-05 13:40:43 +02:00
JIANHONG OU	c8a59adbce	remove the database auto-download for mOTUs.	2022-06-03 14:13:58 -04:00
JIANHONG OU	68d0cc00fa	add motus profile.	2022-05-23 08:05:06 -04:00
James Fellows Yates	06b38f3699	Fix crash, add missing versions	2022-04-23 08:36:01 +02:00
sofstam	d897c922b2	Add centrifuge classificatioN	2022-04-04 13:51:51 +02:00
James Fellows Yates	93aaa9eeac	Clean up AdapterRemoval and remove all debugging dumps	2022-04-01 21:36:22 +02:00
James Fellows Yates	94e5cfef4a	Filter long reads for MALT, bump cpus for FastQC for minigut to pass	2022-03-28 18:20:10 +02:00
James A. Fellows Yates	622fafedc8	Prempt centrifuge database untar crash	2022-03-26 20:22:35 +00:00
sofstam	37a70dc3e3	Merge branch 'dev' into classification_centrifuge	2022-03-25 16:18:35 +01:00
sofstam	3ff54e620e	Add centrifuge classification	2022-03-24 13:02:25 +01:00
James Fellows Yates	07eed435c6	Replace set with explicity assignment	2022-03-21 19:54:51 +01:00
James A. Fellows Yates	631c115e10	Adds PoC of untarring system	2022-03-21 14:58:19 +00:00
James Fellows Yates	c7f022008c	Start getting database prep ready	2022-03-21 15:07:59 +01:00
James Fellows Yates	278f5605ca	Added database preparation and final channel for profiling	2022-02-19 12:36:08 +01:00