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647 commits

Author SHA1 Message Date
James A. Fellows Yates
aa525c6ebf
Allow exit code 1 retry for all java processes 2022-02-06 09:07:53 +01:00
James A. Fellows Yates
81fe720b00
Update eva.config 2022-02-04 09:31:33 +01:00
James A. Fellows Yates
86a9042eac
Update eva.config 2022-02-04 09:25:01 +01:00
James A. Fellows Yates
50aafc6410
Update eva.config 2022-02-03 17:03:10 +01:00
James A. Fellows Yates
8739aabbf0
Bump markduplicates by default 2022-02-02 08:00:13 +01:00
Harshil Patel
9792226f5c
Update genomes.config 2022-01-27 12:45:41 +00:00
Harshil Patel
cd6b8e0f17 Add --nextclade_dataset params 2022-01-17 16:51:55 +00:00
Harshil Patel
f26c465bd4 Add Nextclade genome details to viralrecon genome config 2022-01-17 11:27:10 +00:00
James A. Fellows Yates
5fd5c43906
Update eva.config 2022-01-14 07:03:05 +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
Kevin Brick
1abb1c2d95
Merge pull request #309 from kevbrick/master 
Added config for NIH Biowulf Cluster
 2021-12-20 13:05:19 -05:00
Kevin Brick
82c7d553a7
Update bind-paths 2021-12-20 11:29:09 -05:00
Kevin Brick
87e4ece034
Add files via upload 2021-12-17 00:36:51 -05:00
Venkat Malladi
306c802b4e
Fix name of Params 2021-12-16 09:27:23 -06:00
praveenraj2018
0557f4e062
Renamed star_index directory 2021-12-14 21:15:12 +01:00
Maxime U. Garcia
5e92e2ef11
Update conf/pipeline/rnavar/munin.config 2021-12-14 16:10:31 +01:00
Praveen
cc1fe5b5a0 Addressed review feedback 2021-12-14 03:58:54 +01:00
Praveen
b4d5330c0e Added rnavar pipeline config for Munin 2021-12-14 03:52:37 +01:00
James A. Fellows Yates
55f452d81e
Update eva.config 2021-12-07 09:27:28 +01:00
James Fellows Yates
e8252ad61c Reintroduce bionode8, bump overhead for flagstat 2021-12-03 08:36:31 +01:00
James Fellows Yates
06b40798c0 Exclude bionode8 2021-12-02 10:35:35 +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
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
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
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
Harshil Patel
a098ad9e06 Add Chris as main contact at The Crick 2021-11-03 11:11:05 +00:00
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
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