785 commits

Author	SHA1	Message	Date
James Fellows Yates	58dd9d49c7	Move beforeScript exports to env scope	2022-06-15 15:21:20 +02:00
James Fellows Yates	9ef52af084	Increase overhead	2022-06-03 14:24:27 +02:00
James Fellows Yates	c40ebb9acf	Add overhead for get_software_versions	2022-06-03 14:21:41 +02:00
James Fellows Yates	df0429ce9d	Replace oracle specific _JAVA_OPTIONS to portable JAVA_TOOLS_OPTIONS	2022-06-03 14:20:39 +02:00
James A. Fellows Yates	7353fb257d	Merge pull request #380 from jfy133/taxprofiler ... Add MAG @ EVA profile	2022-06-03 12:54:47 +02:00
James Fellows Yates	5a67eba04c	Add MAG @ EVA profile	2022-06-03 12:41:08 +02:00
Emil Bertilsson	80e2a50a2f	Merge pull request #378 from raysloks/feat/hasta_java_memory_fix ... Feat/hasta java memory fix	2022-05-30 14:40:52 +02:00
Emil	8453f6b41a	Moves qualimap arg to pipeline-specific config	2022-05-30 12:58:12 +02:00
Emil	29fa08c434	Adds _JAVA_OPTIONS to singularity whitelist	2022-05-30 11:07:24 +02:00
Emil	19497a4183	Makes qualimap fix work for most memory amounts	2022-05-30 11:06:48 +02:00
Nicolas Vannieuwkerke	c2b26a734d	automated the internal cache dir location for singularity	2022-05-20 09:48:19 +02:00
Nicolas Vannieuwkerke	cc86e6b270	Added the VSC UGent profile	2022-05-20 09:12:18 +02:00
Sarah Guinchard	be9711731a	Merge pull request #375 from nf-core/ifb_core-config-update ... Ifb core config update	2022-05-13 14:45:44 +02:00
Sarah Guinchard	3538f8511a	removed comment	2022-05-12 11:02:42 +02:00
sofstam	54b3cda34d	Add review suggestion	2022-05-12 11:00:26 +02:00
Sarah Guinchard	6bb7c1a422	Update config file with queue & correct ressources	2022-05-12 10:55:00 +02:00
sofstam	c59149d64c	Update docs for hasta config	2022-05-12 10:47:03 +02:00
James Fellows Yates	e1f780d976	Add taxprofiler for eVA	2022-05-12 07:54:17 +01:00
sofstam	5bc6ed90bd	Add hasta config for taxprofiler	2022-05-11 11:13:31 +02:00
Thiseas C. Lamnidis	d09f5fc116	Update eva.config ... eigenstrat_snp_coverage also loads pandas	2022-05-06 15:12:04 +02:00
James A. Fellows Yates	8fbfcfe256	Merge pull request #371 from jfy133/master ... Rename custom log file for EVA	2022-05-06 14:02:03 +02:00
James A. Fellows Yates	95d18270e8	Update eva.config	2022-05-06 13:57:11 +02:00
Emil	e938f3606f	Removes the new SGE clusterOptions for now	2022-05-05 14:09:45 +02:00
Harshil Patel	20c826fd50	Update retry strategy for preemptible instances on GCP	2022-05-05 11:10:05 +01:00
Emil	8b9744723c	Fixes hasta java memory issues	2022-05-04 14:13:24 +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
Alex Rajewski	69d1a14894	basic Cedars-Sinai HPC config file	2022-04-22 10:17:13 -07:00
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
James A. Fellows Yates	576351219a	Update eva.config	2022-03-29 12:47:46 +02:00
James A. Fellows Yates	9e502025b9	Merge pull request #358 from aidaanva/master ... Update eva.config bigmem.q	2022-03-28 09:11:18 +02:00
Mahesh Binzer-Panchal	3a7f7f431e	Execute sinfo with bash shell	2022-03-25 13:58:37 +00:00
Aida Andrades Valtueña	b9da0b4f00	Update eva.config ... Update eva.config to send big memory jobs (>700G) to the bigmem queue	2022-03-25 09:36:29 +01:00
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	962d86d604	Merge pull request #346 from sagc-bioinformatics/sahmri ... Added SAHMRI profile	2022-03-18 13:01:36 +01:00