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1757 commits 4 branches 0 tags 1.9 MiB
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65 commits

Author SHA1 Message Date
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
lquayle88
a9b62c53e0 Added global institutional and pipeline configs for sbc_sharc 2022-09-13 17:02:44 +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
MaxUlysse
dd1ddf864b update sarek munin config 2020-03-11 14:01:28 +01:00
Adrian Larkeryd
a882b6cbaa adding icr_davros config files generic and sarek 2020-03-04 15:00:33 +00:00
Maxime Garcia
9a8bb12020
Update conf/pipeline/sarek/uppmax.config 2020-02-27 17:22:03 +01:00
Maxime Garcia
8acbdacf03
Update conf/pipeline/sarek/uppmax.config 
Co-Authored-By: Johannes Alneberg <johannes.alneberg@scilifelab.se>
 2020-02-27 17:21:03 +01:00
Maxime Garcia
09ff8f5790
Update conf/pipeline/sarek/uppmax.config 2020-02-27 17:02:31 +01:00
Maxime Garcia
17d6a7e922
Update conf/pipeline/sarek/uppmax.config 2020-02-27 17:02:13 +01:00
Maxime Garcia
ab8998e12b
Update uppmax.config 2020-02-27 16:52:51 +01:00
MaxUlysse
9f74e88041 update file 2020-02-24 14:36:45 +01:00