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Author SHA1 Message Date
Venkat Malladi
1312949768 Merge branch 'azure' of github.com:vsmalladi/configs into azure 2021-11-18 17:55:37 -06:00
Venkat Malladi
46182c7439 Fix markdown linting erros. 2021-11-18 17:55:16 -06:00
Phil Ewels
b25bd1ce42
Update docs/azurebatch.md 2021-11-19 00:54:39 +01:00
Venkat Malladi
72ccd44ad6 Remove storage name. 2021-11-18 17:52:51 -06:00
Venkat Malladi
ed4c1d5f22 Remove work_dir option. 2021-11-18 17:52:24 -06:00
Venkat Malladi
13a8d7aebe Fix spelling. 2021-11-18 15:51:12 -06:00
Venkat Malladi
f25dc57f00 Fix headers. 2021-11-18 15:50:12 -06:00
Venkat Malladi
1dacc2f3fe Fix liniting errors in headers. 2021-11-18 15:49:08 -06:00
Venkat Malladi
845a9ce971 Update Readme with more inforamtion on the options. 2021-11-18 15:47:27 -06:00
Venkat Malladi
219244f1b4 Add in sample datastorage for Illumina Platinum genomes. 2021-11-18 15:28:34 -06:00
Venkat Malladi
b1a9c2e4c6 Add in fake key. 2021-11-18 15:20:59 -06:00
Venkat Malladi
a8075ee938 Fix configuration to pass. 2021-11-18 15:15:23 -06:00
Venkat Malladi
237f91a3b7 Add in minmum config for azure. 2021-11-18 14:51:39 -06:00
Maxime U. Garcia
0866682e9b
Merge pull request #296 from drpatelh/hostnames 
Add Chris as main contact at The Crick
 2021-11-03 13:30:51 +01:00
Harshil Patel
a098ad9e06 Add Chris as main contact at The Crick 2021-11-03 11:11:05 +00:00
Phil Ewels
556a1cf344
Merge pull request #294 from ewels/master 
UPPMAX profile - minor tweaks
 2021-11-03 00:02:17 +01:00
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
448c662d20
Merge pull request #295 from drpatelh/hostnames 
Change params.hostnames from map to string
 2021-11-02 15:29:13 +01:00
Phil Ewels
c842ca70a7 Address review comments 2021-11-02 13:32:19 +01:00
Harshil Patel
7aff8923ea Test remove params.hostnames entirely 2021-11-02 10:52:14 +00:00
Harshil Patel
adeff52f89 Change params.hostnames from map to string 2021-11-02 10:37:53 +00:00
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
Phil Ewels
0600ac1293
Merge pull request #293 from pontus/bugfix/issue_291_part1 
Make memory checks use closed intervals
 2021-11-02 08:54:14 +01:00
Pontus Freyhult
a04b5079f0 Make memory checks use closed intervals 2021-11-02 07:55:52 +01:00
James A. Fellows Yates
5afa43ad15
Merge pull request #289 from jfy133/eva-fix 
Remove broken 1240k profile for eager@EVA
 2021-10-18 11:03:39 +02:00
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
James A. Fellows Yates
7f94989b39
Merge pull request #288 from nf-core/TCLamnidis-patch-1 
added 1240k profile
 2021-10-18 08:45:19 +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
8d68d76a44
Merge pull request #287 from mahesh-panchal/add_snic_tmp 
Add SNIC_TMP to config
 2021-10-11 10:38:50 +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
James A. Fellows Yates
98bbc2b744
Linting 2021-10-08 14:11:39 +02:00
James A. Fellows Yates
b26e495e19
Apply suggestions from code review 2021-10-08 14:08:51 +02:00
pierrespc
2d102eafbc format docs 2021-10-08 13:46:47 +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
4f8b0d6478
Merge pull request #286 from FriederikeHanssen/cfc 
Update sarek - cfc specific config
 2021-10-05 10:50:08 +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
136fd44e0c corrected docs/maestro.config 2021-09-29 13:50:56 +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