phue
bdf4a829b8
roll out iGenomes on cbe
2019-11-26 14:22:16 +01:00
Alexander Peltzer
23f9fd2d73
Merge branch 'master' into master
2019-11-26 14:20:36 +01:00
Maxime Garcia
68c709432f
Apply suggestions from code review
...
Co-Authored-By: Phil Ewels <phil.ewels@scilifelab.se>
2019-11-26 14:17:32 +01:00
Alexander Peltzer
d592c79954
Merge branch 'master' into master
2019-11-26 13:59:06 +01:00
MaxUlysse
ebdfc2a768
fix container/module collision
2019-11-26 11:59:00 +01:00
Maxime Garcia
880551d246
Apply suggestions from code review
2019-11-26 11:58:13 +01:00
Maxime Garcia
f6c2e4c65f
Update docs/pipeline/sarek/munin.md
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Update conf/pipeline/sarek/munin.config
testing out module and containers collision
2019-11-26 11:57:51 +01:00
Maxime Garcia
9d23f7a266
Update conf/pipeline/sarek/munin.config
2019-11-26 11:56:02 +01:00
MaxUlysse
45cec1ac2f
Add specific sarek config base, munin specific sarek config and docs
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rename file
improve configs
remove unnecessary params
2019-11-26 11:52:53 +01:00
MaxUlysse
028008c1d0
improve syntax
2019-11-26 11:48:29 +01:00
Maxime Garcia
93d5156c7d
Update conf/munin.config
2019-11-26 11:48:29 +01:00
MaxUlysse
e98f74e47b
actually belong to nf-core/configs/munin
2019-11-26 11:48:29 +01:00
MaxUlysse
edde1ee64d
fix container/module collision
2019-11-26 11:48:29 +01:00
Maxime Garcia
9a57e487d7
Apply suggestions from code review
2019-11-26 11:48:29 +01:00
Maxime Garcia
b029ccaa59
Update docs/pipeline/sarek/munin.md
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Update conf/pipeline/sarek/munin.config
2019-11-26 11:48:11 +01:00
Maxime Garcia
73047968cf
Update conf/pipeline/sarek/munin.config
2019-11-26 11:25:29 +01:00
MaxUlysse
cd1d0b5f8f
Add specific sarek config base, munin specific sarek config and docs
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rename file
improve configs
remove unnecessary params
2019-11-26 11:25:29 +01:00
Maxime Garcia
1ce8ce0c55
Apply suggestions from code review
2019-11-26 11:00:24 +01:00
MaxUlysse
75c1fd5cd9
fix tests
2019-11-26 10:43:23 +01:00
Alexander Peltzer
b60fa8109e
Shift some configs to params scope
2019-11-26 00:57:10 +01:00
Noirot Céline
ed4436c1a6
Merge branch 'master' into master
2019-11-25 16:24:12 +01:00
noirot
db51c49b2f
Add genotoul config
2019-11-25 14:54:25 +01:00
MaxUlysse
08a6b74825
add new profile to be shared: awsbatch
2019-11-19 14:16:06 +01:00
Alexander Peltzer
bc9ecf50ac
Update binac.config
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Upgrade to 3.4.2
2019-11-11 13:56:17 +01:00
Alexander Peltzer
e66ca6f670
Merge pull request #83 from nf-core/cfc_new_singularity_test
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Update Singularity to 3.4.2 on CFC
2019-11-11 13:55:01 +01:00
Alexander Peltzer
d2603a134e
Add in denbi cloud configs
2019-11-11 12:26:19 +01:00
Alexander Peltzer
426017d727
Merge remote-tracking branch 'upstream/master'
2019-11-11 12:21:53 +01:00
Alexander Peltzer
16a0ba9fd5
Update cfc.config
2019-11-08 10:06:23 +01:00
phue
5a9dbe5d7c
MENDEL is no more
...
the cluster is no longer operational, was replaced by CBE
2019-10-28 14:11:34 +01:00
Alexander Peltzer
eb6d23254d
Fix binac resources
2019-10-28 13:22:12 +01:00
Alexander Peltzer
e557ced184
Update max memory
2019-10-28 13:21:41 +01:00
Alexander Peltzer
06bd1ab79e
Merge branch 'master' into master
2019-10-28 13:21:08 +01:00
Alexander Peltzer
41e607e7f9
Fix expression
2019-10-28 13:17:39 +01:00
Alexander Peltzer
494aa8b53e
Mini fix
2019-10-28 13:15:54 +01:00
Alexander Peltzer
5348b8c609
Revert "BINAC SMP / Short / Long Updates"
2019-10-28 13:12:31 +01:00
Alexander Peltzer
7951805fbf
Merge pull request #43 from apeltzer/master
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BINAC SMP / Short / Long Updates
2019-10-28 13:09:56 +01:00
Alexander Peltzer
83fcc0b2ba
Adjust max memory
2019-10-28 13:09:30 +01:00
phue
18ed48f398
deprecate igenomesIgnore in favor of igenomes_ignore
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keep both for now until all the pipelines have been synced
2019-10-28 11:38:24 +01:00
phue
123f199b68
cbe: dynamic qos logic
2019-10-27 20:44:08 +01:00
Alexander Peltzer
5ec19e3abb
Binac SMP / Long / Short Queue Additions
2019-10-27 13:28:00 +01:00
Maxime Borry
834601f05b
Merge branch 'master' of https://github.com/nf-core/configs
2019-10-25 15:52:23 +02:00
Maxime Borry
7a2fe44b43
resource based queuing
2019-10-25 15:50:49 +02:00
maxibor
5e54912ada
add queue choice
2019-10-25 14:08:02 +02:00
Anthony Bretaudeau
1f2786c78f
add genouest cluster
2019-10-16 18:15:04 +02:00
phue
9b3fda36f6
update singularity version
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singularity/3.1.0 is not available anymore
2019-10-10 21:22:19 +02:00
Sven Fillinger
dc3faf8a5f
Sends weblog messages over HTTPS
2019-10-10 12:56:39 +02:00
Sven Fillinger
855da0cee3
Refactors weblog url
2019-10-08 14:19:42 +02:00
Alexander Peltzer
ed8c9d9e7a
Update cfc.config
2019-10-08 13:20:58 +02:00
Alexander Peltzer
1e54d9510d
Update cfc.config
2019-10-08 13:15:49 +02:00
Alexander Peltzer
865909ac54
Update cfc.config
2019-10-08 13:14:21 +02:00
Alexander Peltzer
5fae33669d
Update cfc.config
...
Try this out 👍
2019-10-08 13:07:28 +02:00
Alexander Peltzer
4555dd7d36
Update conf/cfc.config
2019-10-08 12:51:01 +02:00
Alexander Peltzer
abb6780081
Add Singularity Cache Directory
2019-10-08 12:48:24 +02:00
phue
5e257e7e9a
add cbe profile
2019-09-22 16:45:09 +02:00
Alexander Peltzer
836da97efd
Merge pull request #66 from marchoeppner/ccga-config
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Updating CCGA configs - adding cache dir and mount points
2019-09-03 17:25:34 +02:00
marchoeppner
3b638e9ccd
Fixing typo in ccga_dx config
2019-09-03 15:37:15 +02:00
Szilveszter Juhos
c3c0d088dd
typo
2019-08-16 11:13:32 +02:00
marchoeppner
486cdfce5f
Updating CCGA configs - adding cache dir and mount points
2019-08-07 13:19:16 +02:00
MaxUlysse
4183090379
fix: reduce cpu and mem usage
2019-08-07 12:26:51 +02:00
MaxUlysse
23dd3dd098
Merge branch 'master' of github.com:MaxUlysse/nf-core_configs
2019-08-07 11:56:52 +02:00
MaxUlysse
0bd19517b3
fix: typos
2019-08-07 11:55:56 +02:00
Maxime Garcia
d6a763214c
Update conf/munin.config
...
Co-Authored-By: Harshil Patel <drpatelh@users.noreply.github.com>
2019-08-07 11:47:47 +02:00
Maxime Garcia
12fb2a60c5
Update conf/munin.config
...
Co-Authored-By: Harshil Patel <drpatelh@users.noreply.github.com>
2019-08-07 11:47:41 +02:00
MaxUlysse
332ba0dadb
fix: update and rearrange munin configuration file and docs
2019-08-07 11:10:48 +02:00
Martin Proks
c583aa0233
Added kraken config ( #15 )
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* Added kraken template
* docs: updated some info
* fix: updated igenomes_base path
2019-08-05 11:19:05 +02:00
drpatelh
e0c684ee8f
Aarrrgh pulling configs from master
2019-07-31 23:39:42 +01:00
drpatelh
a692ded933
Remove workDir in czbiohub
2019-07-31 23:30:51 +01:00
drpatelh
daf1b9dcd2
Fix type in uppmax-devel
2019-07-31 22:09:30 +01:00
Remi Planel
1c0d596582
Merge remote-tracking branch 'upstream/master'
2019-07-30 16:15:20 +02:00
Remi Planel
b4cffe0455
Remove buggy cluster option
2019-07-30 15:15:07 +02:00
marchoeppner
b31db18dfb
Adding config file for CCGA dx cluster
2019-07-29 12:08:07 +02:00
Remi Planel
fbb33fde63
Details
2019-07-24 11:43:08 +02:00
Remi Planel
1b30c5a4d2
Add the Pasteur profile
2019-07-24 11:32:02 +02:00
Alexander Peltzer
9106559b2f
Update cfc.config
2019-07-15 17:53:11 +02:00
Olga Botvinnik
474e98daaf
Merge branch 'master' into olgabot/czb-update
2019-07-09 16:02:25 -07:00
marchoeppner
cb507177d5
Updating CCGA config file
2019-07-05 08:03:37 +02:00
Olga Botvinnik
069963ff8a
Make czbiohub_aws_highpriority only set the AWS Batch queue and nothing else
2019-07-03 16:01:47 -07:00
Olga Botvinnik
917ec0863d
add default trimming
2019-07-03 16:01:03 -07:00
Alexander Peltzer
45d36a1506
Update cfc.config
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Add Weblog for CFC cluster
2019-07-03 09:21:16 +02:00
Olga Botvinnik
6a2d2003f0
Add high priority AWS batch queue to CZBiohub AWS
2019-07-01 09:25:46 -07:00
Olga Botvinnik
70b5205d15
Add human salmon index and mouse star index
2019-06-27 15:02:47 -07:00
Olga Botvinnik
d1983f8acd
Use new and improved GENCODE+ERCC annotation
2019-06-26 17:56:26 -07:00
Olga Botvinnik
b0c67e0a9b
Add both seqCenter and seq_center
2019-06-24 17:52:10 -07:00
Olga Botvinnik
acad9ac7e5
Try to clean up czb update
2019-06-24 17:50:36 -07:00
Szilveszter Juhos
f40ed194e3
Using correct reference location for munin
2019-06-24 09:54:37 +02:00
James A. Fellows Yates
505af9a909
Merge pull request #49 from maxibor/master
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Fix queuesize Ccope and Singularity
2019-06-18 20:36:36 +02:00
maxibor
c7eed3fa4c
fix queuesize scope and singularity
2019-06-14 19:16:20 +02:00
Alexander Peltzer
ebe838ac7e
Merge pull request #45 from czbiohub/olgabot/czbiohub
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[WIP] Add CZ Biohub
2019-06-06 13:35:34 +02:00
Olga Botvinnik
3a481402b8
Get czbiohub config to work
2019-06-05 14:42:07 -07:00
Tobias Schraink
4491907f14
updated singularity version in conf/prince.config to reflect version installed on prince
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The prince admins changed the singularity version to 3.2.1 from 3.1.0, making the old version unavailable. To keep this config functional, I updated the version number for singularity.
2019-06-04 12:56:11 -04:00
Alexander Peltzer
515e9484de
Merge pull request #44 from drpatelh/dev
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Add proper nf-core logo
2019-06-01 12:36:57 +02:00
Olga Botvinnik
9c0315addb
Use flat nongzipped files
2019-05-31 13:17:48 -07:00
Olga Botvinnik
1b2fcf5a98
Add author lines
2019-05-31 08:16:51 -07:00
Olga Botvinnik
66eeeebe81
Initial commit of CZBiohub
2019-05-30 11:15:38 -07:00
Alexander Peltzer
441ddbcdab
Newest Update is 3.0.3
2019-05-28 15:25:10 +02:00
maxibor
de1b2aa7d2
remove autoformat added space
2019-04-25 15:50:48 +02:00
maxibor
efd831a8a3
add automounts for singularity
2019-04-25 15:48:20 +02:00
Alexander Peltzer
7d7c18273b
Merge pull request #41 from tobsecret/master
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Added configs for NYU clusters BigPurple (NYU Med) and Prince (NYU main campus)
Last PR merge before Easter holiday ;-)
2019-04-19 00:13:49 +02:00
Tobias Schraink
4ba831705d
added nyu prince and bigpurple md files, added singularity cacheDir to prince and bigpurple configs
2019-04-18 14:13:02 -04:00
maxibor
9d9ac4c3bb
remove whitespace
2019-04-18 11:22:54 +02:00
maxibor
1772f4119c
adding igenomes to shh config
2019-04-18 11:19:53 +02:00
Tobias Schraink
4a915e330a
added warnings to run on SCRATCH
2019-04-17 17:15:16 -04:00
Tobias Schraink
51c2a54399
added nyu prince and bigpurple configs
2019-04-17 16:59:38 -04:00
maxibor
76a5fcf077
switch to queueSize 16 for shh config
2019-03-20 13:44:13 +01:00
maxibor
0929349303
add queueSize limited to 5
2019-03-18 11:13:11 +01:00
James A. Fellows Yates
ecb36dd8c2
Reduced memory and CPUs for cdag compatibility
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Also matches 'fair use' policy
2019-03-14 21:26:43 +01:00
James A. Fellows Yates
3da1373c14
Updated path to centralised singularity cache
2019-03-14 21:16:02 +01:00
Harshil Patel
8bc975c8c3
Merge pull request #33 from ewels/master
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Removed params.config_profile_name, added params.hostnames
2019-03-13 16:49:43 +00:00
Phil Ewels
1191863e1c
Removed params.config_profile_name, added params.hostnames
2019-03-13 17:19:34 +01:00
phue
13df59bfaf
remove singularity support
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reasons:
* the kernel running on the compute nodes does not support overlayfs und thus containers downloaded from
public registries won't run because they lack the /lustre mountpoint
* building containers manually using the Singularity file would work, however nf-core pipelines will stop
providing these files in future releases
2019-03-12 17:57:31 +00:00
Alexander Peltzer
fbf9397182
Bump
2019-03-12 18:48:29 +01:00
Alexander Peltzer
3ee7195fa8
Central resource for both binac and cfc now
2019-03-12 14:58:41 +01:00
Alexander Peltzer
68b759d6ef
Mini Update
2019-03-11 18:12:35 +01:00
Alexander Peltzer
f4f3c4e53b
Roll out binac too
2019-03-11 14:29:42 +01:00
Alexander Peltzer
6b21538062
Rolling out iGenomes now
2019-03-07 16:12:30 +01:00
phue
59887d9bc8
update config for MENDEL cluster
2019-02-27 16:03:26 +00:00
Alexander Peltzer
164ae59568
Update cfc.config
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Please use the newest singularity version 3.0.3!
2019-02-21 10:49:29 +01:00
Alexander Peltzer
d6ea834f40
Update cfc.config
2019-02-21 09:17:28 +01:00
Alexander Peltzer
637ffb782c
Fix CFC config
2019-02-19 17:03:53 +01:00
James A. Fellows Yates
7a51c684f5
Made small SLURM queue change for SHH
2019-01-21 20:31:37 +01:00
Martin Proks
7acd9cf7df
Updating suggested changes
2019-01-11 15:28:10 +01:00
Martin Proks
89dbb6c061
Setting Singularity as default method
2019-01-11 14:37:12 +01:00
Martin Proks
548c8bca3f
Updated munin doc and configuration
2019-01-10 15:46:16 +01:00
Martin Proks
f259178642
Added munin config boilerplate
2019-01-09 17:27:55 +01:00
Phil Ewels
66a08891c7
Documentation tweaks
2019-01-07 14:25:06 +01:00
Harshil Patel
59bc3b43be
Update crick.config
2019-01-07 11:35:49 +00:00
Harshil Patel
f81c67627e
Update crick.config
2019-01-07 11:18:01 +00:00
Alexander Peltzer
d4ea56aaae
Update UCT_Hex profile
2019-01-07 12:14:04 +01:00
Alexander Peltzer
2b814041ee
Add in both uppmax profiles
2019-01-04 16:33:54 +01:00
Alexander Peltzer
6f7a3cc422
Add Hebbe
2019-01-04 16:30:40 +01:00
Alexander Peltzer
e07d8bd687
Get rid of header in CRICK config
2019-01-04 16:29:49 +01:00
Alexander Peltzer
aca790bb4b
Add CCGA Profile
2019-01-04 16:28:41 +01:00
Alexander Peltzer
7af6b48b4d
Adjust general usage to separate params section
2019-01-04 14:55:22 +01:00
Alexander Peltzer
9c97680d4c
Add UZH
2019-01-04 14:49:52 +01:00
Alexander Peltzer
bc8e05f4b3
Add Phoenix
2019-01-04 14:48:14 +01:00
Alexander Peltzer
6ae7d02b14
Add Mendel
2019-01-04 14:46:30 +01:00
Alexander Peltzer
078272745a
Update BINAC, CFC, SHH COnfig profiles
2019-01-04 14:42:09 +01:00
Alexander Peltzer
87cea82c43
Use james github handle
2019-01-04 10:21:16 +01:00
Alexander Peltzer
a78fe147f0
Add more details on config profiles
2019-01-04 10:19:39 +01:00
Alexander Peltzer
1051339461
Remove base config stuff
2019-01-03 16:02:07 +01:00
Alexander Peltzer
98fca8a1ef
Add SHH Configuration
2019-01-03 16:01:06 +01:00
phue
5c609859c5
add config for MENDEL cluster
2018-12-04 16:58:33 +01:00
Harshil Patel
ddc0bbd7b3
Update phoenix.config
2018-11-26 23:31:44 +00:00
Alexander Peltzer
42ed4b9da4
Add Phoenix configs
2018-11-27 00:02:40 +01:00
Harshil Patel
2c513e5266
Update binac.config
2018-11-26 22:47:36 +00:00
Phil Ewels
e38e9327f4
Some tidying
2018-11-26 17:32:06 +01:00
drpatelh
d52db66077
Added existing configs from all pipelines
2018-11-23 15:56:34 +00:00