55 commits

Author	SHA1	Message	Date
James A. Fellows Yates	c1425c6c01	Merge pull request #364 from jfy133/eva-update ... Update eager @ eva.config to allow retry on post-processing FASTQ	2022-04-22 11:47:10 +02:00
James A. Fellows Yates	a086878c0b	Update eva.config	2022-04-22 10:47:04 +02:00
James A. Fellows Yates	44238471cf	Update eva.config	2022-03-31 13:12:50 +02:00
James Fellows Yates	2277b541a3	Re-add bash bin specification	2022-03-31 11:06:53 +02:00
James A. Fellows Yates	8ad4ddac6a	Merge branch 'master' into fix-eva	2022-03-29 12:50:54 +02:00
James Fellows Yates	3d2a612b39	Remove setting of bash in clusterOotions	2022-03-29 12:48:37 +02:00
James A. Fellows Yates	1b5037ce5e	Update eva.config	2022-03-15 07:49:06 +01:00
James A. Fellows Yates	1565b2ce63	Update eva.config	2022-03-15 07:42:23 +01:00
James A. Fellows Yates	f725b6c431	Apply suggestions from code review	2022-03-15 07:36:34 +01:00
James A. Fellows Yates	4670f8bf0c	Update eva.config	2022-03-14 14:56:01 +01:00
James A. Fellows Yates	5547e45ab5	Merge branch 'master' into jfy133-patch	2022-03-02 08:28:22 +01:00
James A. Fellows Yates	46f046d477	Update eva.config	2022-02-28 14:00:37 +01:00
James Fellows Yates	88ddc9eee7	fffff	2022-02-10 11:34:57 +01:00
James Fellows Yates	d7d0f5cecc	Change base time	2022-02-10 11:32:49 +01:00
James Fellows Yates	dbd78f8075	Re add .	2022-02-10 11:26:18 +01:00
James Fellows Yates	dd94895f16	remove quotes	2022-02-10 11:22:45 +01:00
James Fellows Yates	39c2d9b25b	Oops	2022-02-10 11:19:16 +01:00
James Fellows Yates	c0ee3225ad	Add times for 365d	2022-02-10 11:02:52 +01:00
Thiseas C. Lamnidis	fa4075c2a0	Removed all time limits	2022-02-10 10:00:18 +01:00
James A. Fellows Yates	2b06293f64	Read add empty BAM exit code for qualitmap 255	2022-02-08 11:15:17 +01:00
James A. Fellows Yates	8c5a54ac9f	Update conf/pipeline/eager/eva.config	2022-02-06 19:37:53 +01:00
James A. Fellows Yates	aa525c6ebf	Allow exit code 1 retry for all java processes	2022-02-06 09:07:53 +01:00
James A. Fellows Yates	81fe720b00	Update eva.config	2022-02-04 09:31:33 +01:00
James A. Fellows Yates	86a9042eac	Update eva.config	2022-02-04 09:25:01 +01:00
James A. Fellows Yates	50aafc6410	Update eva.config	2022-02-03 17:03:10 +01:00
James A. Fellows Yates	e02196d6ad	Update eva.config	2022-02-03 17:02:34 +01:00
James A. Fellows Yates	0e41349324	Update eva.config	2022-02-03 17:01:54 +01:00
James Fellows Yates	2562a2f563	Remove virtual free	2022-02-02 08:06:00 +01:00
James A. Fellows Yates	8739aabbf0	Bump markduplicates by default	2022-02-02 08:00:13 +01:00
James A. Fellows Yates	5fd5c43906	Update eva.config	2022-01-14 07:03:05 +01:00
James A. Fellows Yates	55f452d81e	Update eva.config	2021-12-07 09:27:28 +01:00
James Fellows Yates	e8252ad61c	Reintroduce bionode8, bump overhead for flagstat	2021-12-03 08:36:31 +01:00
James Fellows Yates	06b40798c0	Exclude bionode8	2021-12-02 10:35:35 +01:00
James A. Fellows Yates	ffdb0a937f	Take previous working one I think	2021-10-18 10:58:06 +02:00
James A. Fellows Yates	b269a577e6	Revert 1240k	2021-10-18 10:52:28 +02:00
Thiseas C. Lamnidis	e741ecb7a7	Update eva.config	2021-10-13 13:04:41 +02:00
Thiseas C. Lamnidis	92648c1c1f	added 1240k profile	2021-10-12 15:12:49 +02:00
James A. Fellows Yates	a7b1183065	Remove 1CPU for host removal fastq	2021-09-14 11:52:21 +02:00
James A. Fellows Yates	7c639ac934	Bump lib merge further	2021-09-09 14:47:20 +02:00
James A. Fellows Yates	0603aba342	Remove debugging stuff	2021-09-09 13:54:01 +02:00
James A. Fellows Yates	7ec12b6736	Update eva.config	2021-09-09 13:10:05 +02:00
James A. Fellows Yates	4286a3a342	Bump additional library merge memor	2021-09-08 15:16:40 +02:00
James A. Fellows Yates	59a0901b68	Add library merge steps to have overhead	2021-09-05 12:07:53 +02:00
James A. Fellows Yates	94cbb031c6	Update eva.config	2021-08-30 13:29:44 +02:00
James A. Fellows Yates	5fbd938bc1	Export user env too	2021-08-27 10:08:20 +02:00
James A. Fellows Yates	6701354060	Add genotyping_ug to SGE fixes	2021-08-20 10:11:11 +02:00
James Fellows Yates	b0e344846d	Changes after code review from @aidaanva	2021-08-04 10:37:49 +02:00
James Fellows Yates	76fc461670	Try new strategy for SGE/JAVA bs	2021-08-04 10:14:56 +02:00
James A. Fellows Yates	00491de038	Update eva.config	2021-08-03 13:54:14 +02:00
James A. Fellows Yates	5f4b915ae8	Update eva.config	2021-06-29 11:31:00 +02:00