244 commits

Author	SHA1	Message	Date
Emil Bertilsson	72e995f326	Adds generic fix for java memory issue on slurm	2022-06-09 10:28:20 +02:00
Emil	8453f6b41a	Moves qualimap arg to pipeline-specific config	2022-05-30 12:58:12 +02:00
Thiseas C. Lamnidis	209601f782	missing bracket	2022-05-04 13:08:13 +02:00
Thiseas C. Lamnidis	a42c4344ad	Exclude bionode 06 for software versions	2022-05-03 18:30:42 +02:00
Thiseas C. Lamnidis	79e227aa4e	Update eva.config	2022-05-03 16:42:21 +02:00
Thiseas C. Lamnidis	085726d081	Update eva.config	2022-05-03 16:36:05 +02:00
Thiseas C. Lamnidis	4592969613	memory for get_software_versions in MB.	2022-05-03 16:30:04 +02:00
Thiseas C. Lamnidis	79ad571319	Update eva.config	2022-05-03 16:25:48 +02:00
Thiseas C. Lamnidis	04226692fe	Update eva.config	2022-05-03 16:21:35 +02:00
Thiseas C. Lamnidis	57095fe79f	Update eva.config ... Set max heap size for java jobs in `get_software_versions`. Limited OpenBLAS threading for python jobs that use numpy/pandas.	2022-05-03 16:12:20 +02:00
James A. Fellows Yates	b5d9b79377	Merge branch 'nf-core:master' into master	2022-05-02 13:59:18 +02:00
James A. Fellows Yates	bf658abc77	Update eva.config	2022-05-02 13:59:13 +02:00
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
Praveen Raj S	edaad1cd18	Update: sentieon version ... Sentieon version has been updated to 202112.02.	2022-04-07 12:36:01 +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
b97pla	9a6cdfc21e	removed process-specific requirements for sarek, request miarka high-mem node	2022-03-24 14:25:43 +01:00
b97pla	5466d927f1	added requirements for uppmax cluster miarka	2022-03-23 15:29:40 +01:00
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	975fca6721	Apply suggestions from code review	2022-03-07 13:51:00 +01:00
James Fellows Yates	70318c3b2a	Tweak eager settigs	2022-03-03 14:29:30 +01:00
ilight1542	5a0543e4ac	Merge branch 'rnaseq_mpcdf' into mpcdf_eager_config_update	2022-03-03 14:17:18 +01:00
ilight1542	25c644abb7	modified mpcdf configs (general + eager)	2022-03-03 13:55:02 +01:00
James A. Fellows Yates	17312604cf	Update mpcdf.config	2022-03-03 12:25:06 +01:00
James Fellows Yates	94f8cbcb84	Add rnaseq pipeline specific config for MPCDF	2022-03-03 12:20:02 +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	ea052a7b67	Merge pull request #334 from jfy133/eva-update ... eva: generalise custom SGE mem flag	2022-03-01 09:23:04 +01:00
James A. Fellows Yates	46f046d477	Update eva.config	2022-02-28 14:00:37 +01:00
Mei Wu	dcba537d15	picard md is single threaded	2022-02-21 16:19:17 +01:00
Combiz Khozoie	2d434c6ee5	Merge pull request #321 from nf-core/combiz-patch-1 ... Imperial config updates	2022-02-11 14:49:30 +00:00
Maxime U. Garcia	4a936a685e	Merge pull request #317 from nf-core/praveenraj2018-patch-1 ... Added genome parameter	2022-02-11 15:33:18 +01:00
Combiz Khozoie	a77f718ae2	Merge pull request #330 from nf-core/master ... Pulling master to branch	2022-02-11 14:18:01 +00:00
Harshil Patel	8fa6ab9b35	Merge pull request #323 from stevin-wilson/patch-1 ... Added ARTIC v4.1 primer set information	2022-02-10 19:17:47 +00:00
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
Stevin Wilson	dbb71161c5	Added ARTIC v4.1 primer set information	2022-02-04 15:31:51 -05:00