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Author SHA1 Message Date
James A. Fellows Yates
71b17ff970
Merge pull request #301 from jfy133/eva 
eager@eva: and bump the second samtools_flagstat process overhead 🙄
 2021-12-07 11:04:33 +01:00
James A. Fellows Yates
55f452d81e
Update eva.config 2021-12-07 09:27:28 +01:00
James A. Fellows Yates
f7b5a8e800
Merge pull request #300 from jfy133/eva 
eager @ eva: reintroduce bionode8, bump overhead for flagstat
 2021-12-03 11:16:24 +01:00
James Fellows Yates
e8252ad61c Reintroduce bionode8, bump overhead for flagstat 2021-12-03 08:36:31 +01:00
James A. Fellows Yates
f8246b8554
Merge pull request #299 from jfy133/eva 
Exclude bionode8 for eager@eva
 2021-12-02 10:57:44 +01:00
James Fellows Yates
06b40798c0 Exclude bionode8 2021-12-02 10:35:35 +01:00
Venkat Malladi
7a49a66b36
Merge pull request #298 from vsmalladi/azure 
Fix Azure Markdown
 2021-11-18 23:52:24 -06:00
Venkat Malladi
d722e7206e Fix readme to remove blob account. 2021-11-18 18:06:54 -06:00
Venkat Malladi
c0bf71bb6c Merge branch 'master' into azure 2021-11-18 18:06:04 -06:00
Phil Ewels
0725e8d382
Merge pull request #225 from jfy133/doc-update 
Make more explicit which files you must update
 2021-11-19 00:56:50 +01:00
Phil Ewels
4785ceccba
Merge pull request #245 from ikeller/unibe_ibu 
Unibe ibu
 2021-11-19 00:56:25 +01:00
Phil Ewels
291fcb20a5
Merge pull request #297 from vsmalladi/azure 
Add in template for Azure Workflow
 2021-11-19 00:55:54 +01:00
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
Phil Ewels
286fa6753a
Apply suggestions from code review 2021-11-19 00:07:33 +01:00
Phil Ewels
e090bbd5fe
Merge pull request #241 from asafpr/master 
replaced owner in JAX
 2021-11-19 00:03:11 +01:00
Phil Ewels
a26b3bf1e3
Merge branch 'master' into unibe_ibu 2021-11-19 00:02:30 +01:00
Phil Ewels
15080d958e
Merge pull request #283 from aunderwo/master 
change max_time diretcive in the correct place
 2021-11-19 00:00:52 +01:00
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