73 commits

Author	SHA1	Message	Date
ameynert	70e3eafeb1	Merge pull request #6 from nf-core/master ... Merge base repository into fork	2022-10-26 16:25:37 +02:00
lquayle88	584052cfff	Revised base and all pipeline configs to provide memory on per core basis	2022-10-04 09:12:29 +01:00
lquayle88	3f2ffa314d	Revised base and sarek configs to provide memory on per core basis	2022-10-04 00:25:16 +01:00
lquayle88	e7ac3ecd19	Modified resource requests in sbc_sharc.config for sarek	2022-10-02 00:24:39 +01:00
lquayle88	9b451b53b7	Increased cpus and memory for GATK4_MARKDUPLICATES in sbc_sharc.config for sarek	2022-10-01 23:31:51 +01:00
lquayle88	10c1490265	Increased memory and time for GATK4_MARKDUPLICATES in sbc_sharc.config for sarek	2022-10-01 23:15:13 +01:00
lquayle88	dbb3b3b44b	Reinstated maxRetries and increased memory for GATK4_MARKDUPLICATES in sbc_sharc.config for sarek	2022-10-01 07:45:28 +01:00
lquayle88	8103718389	Reduced maxRetries upon error in sbc_sharc.config for sarek	2022-09-30 16:54:48 +01:00
lquayle88	c42a5a9a94	Updated resources requested by pipelines	2022-09-23 17:01:58 +01:00
lquayle88	ab1ad832df	Updated resource requests for compatibility with high memory nodes	2022-09-23 13:18:50 +01:00
lquayle88	7e34beb3c9	Updated resource requests for compatibility with general worker nodes	2022-09-23 11:08:39 +01:00
lquayle88	55971bb94d	Modularised error handling strategy to per pipeline basis	2022-09-16 17:29:08 +01:00
ameynert	9167e81214	Added other Java processes with memory overhead, sorted alphabetically	2022-09-14 09:07:09 +01:00
lquayle88	a9b62c53e0	Added global institutional and pipeline configs for sbc_sharc	2022-09-13 17:02:44 +01:00
ameynert	91ef9a3241	Added another Java process with overhead	2022-09-13 09:27:13 +01:00
ameynert	a808933da8	Added another Java process that needs memory overhead	2022-09-09 08:37:21 +01:00
ameynert	29a0b30d85	Updated process names to Sarek 3	2022-09-07 16:00:52 +01:00
Simon Pearce	2c738cae33	Update crukmi.config	2022-09-01 11:24:11 +01:00
Simon Pearce	a8faeda141	Update crukmi.config	2022-09-01 11:23:07 +01:00
SPearce	800931bff2	Add Sarek specific config	2022-09-01 11:13:23 +01:00
Praveen Raj S	edaad1cd18	Update: sentieon version ... Sentieon version has been updated to 202112.02.	2022-04-07 12:36:01 +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
Maxime U. Garcia	61682f33b3	Merge pull request #310 from nf-core/praveenraj2018-patch-1 ... Updated sentieon version through a new module file	2022-01-10 12:04:20 +01:00
ameynert	0f56588acc	Added memory & cluster options specification for eddie sarek config	2022-01-06 10:15:34 +00:00
praveenraj2018	53ab5ee34f	Updated sentieon version through a new module file ... A local module file has been created to run the latest version of Sentieon. Doing this change, as the new version of Sentieon has only a dependency library update, hence it should not break the Sentieon pipeline. Tested locally with a test.conf having the new process block.	2021-12-21 15:21:59 +01:00
Rike	f6e16f2872	Add check_resource to respect max_resource/max_cpus	2021-10-04 10:14:02 +02:00
MaxUlysse	73fcc4495a	feat: update owner of profile	2021-05-19 20:46:52 +02:00
Gisela Gabernet	4e9e5d2c67	Merge branch 'master' into cfc_sarek	2021-04-23 16:47:04 +02:00
ameynert	e5f2a63079	Java overhead processes list updated ... Added all processes calling GATK for Mutect2 variant calling	2021-03-30 16:21:53 +01:00
ameynert	adfb5366b9	Java overhead process list updated ... Added HaplotypeCaller and GenotypeGVCFs to set of processes that need Java overhead	2021-03-30 16:15:17 +01:00
ameyner2	da8cf2f207	Added pipeline-specific config files for rnaseq and sarek	2021-03-24 10:46:26 +00:00
Rike	6221b67bcf	Give Strelka a complete compute node	2021-03-18 11:11:02 +01:00
Rike	b1846af9d3	reduce mapping resource further to compute node	2021-03-18 11:10:00 +01:00
FriederikeHanssen	67c93a4743	Update conf/pipeline/sarek/cfc.config ... Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>	2021-03-18 11:06:38 +01:00
Rike	b70097e495	remove new line	2021-03-17 15:46:18 +01:00
Rike	bb124a9be8	Reduce vc to run on compute	2021-03-11 16:11:41 +01:00
FriederikeHanssen	79ddbe1fea	Add missing bracket	2021-03-11 09:29:03 +01:00
FriederikeHanssen	0057132e02	remove check_reource statement	2021-03-11 09:27:08 +01:00
FriederikeHanssen	eb9012919c	Set values for processes with max_mem/max_cpus	2021-03-10 11:16:18 +01:00
MaxUlysse	8c0cc4b9ec	code polishing	2020-09-25 09:57:50 +02:00
MaxUlysse	81f910cc95	add specific BamQC config	2020-09-25 09:49:43 +02:00
MaxUlysse	fbe7bd133a	update uppmax specific sarek config	2020-09-25 08:33:53 +02:00
Alexander Peltzer	f877644059	Merge branch 'master' into master	2020-05-29 11:43:47 +02:00
Maxime Garcia	34dc18faf6	Update uppmax.config	2020-04-09 11:35:37 +02:00
Adrian Larkeryd	405801638a	icr_davros sarek config description	2020-04-08 11:56:17 +01:00
MaxUlysse	db2dd4458b	Merge remote-tracking branch 'upstream/master' into UPPMAX	2020-03-30 16:41:08 +02:00
MaxUlysse	8b570507cd	update s	2020-03-30 16:40:11 +02:00
Maxime Garcia	123132d89a	Update munin.config ... fix typo	2020-03-12 17:23:55 +01:00
Maxime Garcia	b6d52fdb89	Update conf/pipeline/sarek/munin.config	2020-03-11 15:48:29 +01:00