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602 commits

Author SHA1 Message Date
Phil Ewels
501db6bd2b
Update conf/uppmax.config 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2021-11-02 23:55:27 +01:00
Phil Ewels
c842ca70a7 Address review comments 2021-11-02 13:32:19 +01:00
Phil Ewels
9a17fdb6d9
Update conf/uppmax.config 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2021-11-02 09:58:04 +01:00
Phil Ewels
c7dc9aa892 UPPMAX profile - minor tweaks 
* Only one params block instead of two
* Return only one 'grep' result and don't pipe to 'head'
* Use .startsWith instead of regex matching
* Print detected cluster name in the profile description
 2021-11-02 09:15:01 +01:00
Pontus Freyhult
a04b5079f0 Make memory checks use closed intervals 2021-11-02 07:55:52 +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
Mahesh Binzer-Panchal
ac815ce790
Merge branch 'master' into add_snic_tmp 2021-10-11 09:57:49 +02:00
Pontus Freyhult
33ae41bc91
Merge pull request #226 from pontus/master 
UPPMAX: Allow jobs needing more memory than thin nodes, pick up cluster info through slurm
 2021-10-10 12:05:07 +02:00
James A. Fellows Yates
73b6b74c69
Merge pull request #279 from pierrespc/master 
Added Configuration files for running in Maestro HPC at Pasteur Institute, Paris
 2021-10-08 19:15:47 +02:00
Mahesh Binzer-Panchal
747a89b4c5
Update conf/uppmax.config 2021-10-08 13:40:59 +02:00
pierrespc
035ab61f61 added unlimitedtime profile to maestro; changed cache for bwa process 2021-10-08 09:05:46 +02:00
Mahesh Binzer-Panchal
e557e94bfb Add SNIC_TMP to config 2021-10-07 16:05:03 +02:00
FriederikeHanssen
f1756ba121
Merge branch 'nf-core:master' into cfc 2021-10-04 18:04:18 +02:00
pierrespc
1621585558 improving documentation 2021-10-04 16:08:33 +02:00
pierrespc
e5d4a357c5 clean doc 2021-10-04 15:08:01 +02:00
Falko Hofmann
0950eb3518
Merge pull request #251 from phue/cbe_singularity_workaround 
cbe: send SIGUSR2 upon job termination
 2021-10-04 13:24:53 +02:00
Rike
f6e16f2872 Add check_resource to respect max_resource/max_cpus 2021-10-04 10:14:02 +02:00
pierrespc
f6266879d6 edited maestronuclear and maestromitocondrial configs. The latter has not been optimized yet 2021-09-29 13:47:35 +02:00
pierrespc
b71df6fe57 renamed eager pipeline config file 2021-09-29 13:22:07 +02:00
pierrespc
9ea3e2096a long and normal qos profiles defined now in an unique maestro config file. maestro.config also defined in pipeline/eager for ressources assignation to specific processes 2021-09-29 13:11:14 +02:00
Bjørn Peare Bartholdy
e750a6d445
Update conf/alice.config 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2021-09-28 13:34:12 +02:00
Bjørn Peare Bartholdy
197bd6cfb1
Merge branch 'nf-core:master' into master 2021-09-28 12:09:50 +02:00
bbartholdy
b6ccb46383 add ALICE profile 2021-09-28 12:08:27 +02:00
Mei Wu
79a79f7d8d added pipeline-specific config 2021-09-28 10:38:25 +02:00
Mei Wu
c2d74b290a fix md 2021-09-27 16:25:02 +02:00
Mei Wu
a8a2027f70
Merge branch 'master' into hasta 2021-09-27 16:12:23 +02:00
Mei Wu
06fac1dcfc initial commit 2021-09-27 16:05:32 +02:00
Mei Wu
ae0adb056f initial commit 2021-09-27 16:05:19 +02:00
Anthony Underwood
6a970dc4a8
update max time for long queue 2021-09-23 11:59:45 +01:00
Patrick Hüther
1cbe2759c4
fix invalid rapid qos selection 
it only applies to the c partition
 2021-09-22 11:54:27 +02:00
pierrespc
3e22b85b02 maestro only for normal qos 2021-09-22 10:13:46 +02:00
Anthony Underwood
50df2105fb update long jobs to be submitted to the long queue 2021-09-21 14:42:59 +01:00
pierrespc
3b593d46ec merged two pasteur config files for maestro 2021-09-20 15:14:50 +02:00
Harshil Patel
5068e4806f
Merge pull request #271 from theoportlock/master 
Adds Rosalind config for KCL!
 2021-09-17 13:36:19 +01:00
Harshil Patel
3b95fd9ee3
Update conf/rosalind.config 2021-09-17 13:15:09 +01:00
theoportlock
9116a09afe Fixes formatting and ignore_params 2021-09-17 13:21:32 +02:00
pierrespc
4614ff6f45 change max mem in Normal 2021-09-16 16:50:45 +02:00
pierrespc
de2a745fde change type in Normal name 2021-09-16 16:48:26 +02:00
pierrespc
482e7cf8de 2 config files for Maestro HPC at Pasteur Institute, Paris 2021-09-16 12:40:56 +02:00
Marc Trunjer Kusk Nielsen
a55c3c04eb
Update computerome.config 
Adding genomes and modules back into schema_ingore_params to avoid warnings about unexpected parameters.
 2021-09-15 19:54:51 +02:00
Marc Trunjer Kusk Nielsen
8b29b5584e
Update computerome.config 2021-09-15 14:20:02 +02:00
Marc Trunjer Kusk Nielsen
ab8a9ad0b8
Update computerome.config 2021-09-15 13:27:23 +02:00
theoportlock
9c97220919 Merge branch 'master' of https://github.com/theoportlock/configs 2021-09-15 11:43:09 +02:00
theoportlock
3c86f8f47c Removes the broken clusterOptions 2021-09-15 11:42:43 +02:00
Marc Trunjer Kusk Nielsen
aad70fe86d
Merge branch 'nf-core:master' into computerome 2021-09-15 11:08:48 +02:00
Marc Trunjer Kusk Nielsen
29003e13f1
Update computerome.config 2021-09-15 10:22:57 +02:00
James A. Fellows Yates
a7b1183065
Remove 1CPU for host removal fastq 2021-09-14 11:52:21 +02:00