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Author SHA1 Message Date
Maxime Garcia
8acbdacf03
Update conf/pipeline/sarek/uppmax.config 
Co-Authored-By: Johannes Alneberg <johannes.alneberg@scilifelab.se>
 2020-02-27 17:21:03 +01:00
Maxime Garcia
09ff8f5790
Update conf/pipeline/sarek/uppmax.config 2020-02-27 17:02:31 +01:00
Maxime Garcia
17d6a7e922
Update conf/pipeline/sarek/uppmax.config 2020-02-27 17:02:13 +01:00
Maxime Garcia
ab8998e12b
Update uppmax.config 2020-02-27 16:52:51 +01:00
MaxUlysse
a8d338d2aa Merge branch 'Uppmax' of github.com:MaxUlysse/nf-core_configs into Uppmax 2020-02-24 14:37:27 +01:00
MaxUlysse
9f74e88041 update file 2020-02-24 14:36:45 +01:00
Marc Hoeppner
6c5a5c8bcb Removing old CCGA profile from docs and linting 
Removing CCGA profile from master config

Removing CCGA profile from master config
 2020-02-24 12:16:33 +01:00
Maxime Garcia
9b897345da
Update conf/pipeline/sarek/uppmax.config 
Co-Authored-By: Phil Ewels <phil.ewels@scilifelab.se>
 2020-02-21 08:16:31 +01:00
Maxime Garcia
08e2804b37
Merge branch 'master' into Uppmax 2020-02-20 17:18:46 +01:00
MaxUlysse
aa905cd645 add UPPMAX specific sarek config 2020-02-20 17:14:18 +01:00
Daniel Straub
744db30da4
Update binac.config 
This is now close to optimal I think.
 2020-02-19 11:27:02 +01:00
marchoeppner
0830203b70 Adding new CCGA Med Cluster to profiles 
Updating README and fixing linting errors in CCGA_MED profile

Fixing order in profile queue and removed leading slash from readme for ccga profile docs

Fixing order in profile queue and removed leading slash from readme for ccga profile docs
 2020-02-11 11:12:51 +01:00
Daniel Straub
b7be65a31e
Cleanup config 2020-02-07 14:53:43 +01:00
Daniel Straub
7346bffdc8
Update binac.config 
Processes that ask for 128 Gb are queuing forever when on short queue, but executed when send to smp queue.
 2020-01-28 08:48:34 +01:00
James A. Fellows Yates
638758423a
Restricts MALT re-tries and hardcodes resources so cannot go above SDAG max 2019-12-21 20:55:54 +01:00
drpatelh
67c231d05c Change igenomes path 2019-12-18 10:54:23 +00:00
drpatelh
089b5b8e3b Update config 2019-12-12 13:44:37 +00:00
drpatelh
65c5668568 Update config 2019-12-12 13:02:44 +00:00
Maxime Garcia
d36172d4cf
Merge pull request #110 from MaxUlysse/MUNIN 
fix issue with withLabel selector
 2019-12-12 13:03:23 +01:00
MaxUlysse
2bf66514c5 fix issue with withLabel selector 2019-12-12 11:50:10 +01:00
Alexander Peltzer
a6d08ed646
Adjust custom pipeline config for ampliseq on BINAC 2019-12-11 16:09:44 +01:00
Alexander Peltzer
49cd35918a
Remove whitespace 2019-12-11 15:59:58 +01:00
Alexander Peltzer
5e6981d0ee
Export TZ in binac config 2019-12-11 15:59:25 +01:00
Alexander Peltzer
ac90acf470
Update envWhiteList for Binac Profile for testing purposes 
Add envWhitelist for TZ to fix https://github.com/nf-core/ampliseq/issues/114
 2019-12-11 14:26:57 +01:00
James A. Fellows Yates
0beb98696f
Merge branch 'master' into master 2019-12-06 19:31:24 +01:00
James A. Fellows Yates
8747be8120
More tweaks, nextflow appears to add a little extra? 2019-12-06 19:27:16 +01:00
James A. Fellows Yates
5c6760b2f0
Tweak back again 2019-12-06 19:25:07 +01:00
James A. Fellows Yates
46f6d20a77
Put parameters back to correct levels 2019-12-06 19:13:29 +01:00
James A. Fellows Yates
18931763fa
Add space? 2019-12-06 19:11:08 +01:00
James A. Fellows Yates
f59443daf0
Update shh.config 2019-12-06 19:09:20 +01:00
James A. Fellows Yates
1ab1370872
Try to make resources satisfiable 2019-12-06 19:06:05 +01:00
James A. Fellows Yates
6e596d1730
Fix stupid wrong bracket typo -.- 2019-12-06 18:37:39 +01:00
James A. Fellows Yates
b28e1a0905
Wrong bracket typo fix -.- 2019-12-06 18:34:18 +01:00
Alexander Peltzer
1f7940c2ee
Merge pull request #104 from jfy133/master 
Attempt to fix process specific configs with pipeline specific configs
 2019-12-06 17:16:37 +01:00
jfy133
e8b4675692 Cleanup and tweaking 2019-12-06 13:17:31 +01:00
Maxime Garcia
9497b78149
Merge pull request #100 from MaxUlysse/UPPMAX 
Improve UPPMAX configs
 2019-12-06 10:52:44 +01:00
Maxime Garcia
14864bb80b
Update conf/uppmax.config 2019-12-06 10:31:56 +01:00
Alexander Peltzer
da547b4ce3
Merge pull request #102 from phue/cbe_singularity 
cbe: load singularity/3.4.1
 2019-12-06 10:21:55 +01:00
James A. Fellows Yates
0033b74e4e
Update shh.config 2019-12-05 18:08:39 +01:00
James A. Fellows Yates
dc0f1dfb40
Update shh.config 2019-12-05 17:58:49 +01:00
James A. Fellows Yates
b1a8b45aa0
Maybe typo? 2019-12-05 17:52:53 +01:00
jfy133
731372dac2 Added SHH specific EAGER configuration 2019-12-05 17:01:10 +01:00
phue
381c60e7b7 cbe: load singularity/3.4.1 2019-12-05 16:06:32 +01:00
MaxUlysse
a63ec24626 Merge branch 'UPPMAX' of github.com:MaxUlysse/nf-core_configs into UPPMAX 2019-12-05 15:18:04 +01:00
MaxUlysse
99afe86ea9 update docs 2019-12-05 15:18:01 +01:00
MaxUlysse
f41d325873 automatic configs work on all nodes 2019-12-05 15:07:59 +01:00
Maxime Garcia
78826c9d4e
Merge branch 'master' into UPPMAX 2019-12-05 12:52:34 +01:00
Alexander Peltzer
9cdb915efb
Merge pull request #101 from jfy133/master 
Condensing SHH profile(s) with sub-profiles
 2019-12-05 12:51:31 +01:00
MaxUlysse
cf6e00d9f5 better match for hostname 2019-12-05 12:46:32 +01:00
MaxUlysse
20e451be3b actually define hostname 2019-12-05 12:45:30 +01:00
MaxUlysse
0211b33a55 trying automatic configuration based on hostname 2019-12-05 12:41:18 +01:00
James A. Fellows Yates
842642a2bb
Apply suggestions from code review 
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
 2019-12-05 12:23:36 +01:00
James A. Fellows Yates
678a3841b6
Update conf/shh.config 
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
 2019-12-05 12:23:06 +01:00
jfy133
54dafbcfa3 Condensing SHH profiles following https://github.com/nf-core/configs/pull/100 2019-12-05 12:09:11 +01:00
MaxUlysse
cdbdbee0eb replace -profile uppmax_devel by -profile uppmax,devel 2019-12-05 11:49:44 +01:00
Sabrina Krakau
2eed8f7429 Lowered max. memory for cfc 2019-11-28 12:49:02 +01:00
Olga Botvinnik
f57e00e87d
Set awsqueue parameter properly 2019-11-27 15:57:09 -08:00
Alexander Peltzer
4f77eae5cf
Mini adjustment for highmem queue on denbi 2019-11-27 14:23:01 +01:00
Maxime Garcia
2669401a72
Merge branch 'master' into sarek 2019-11-27 13:27:43 +01:00
Alexander Peltzer
5e0e3e0567
Merge pull request #96 from jfy133/master 
Splitting SHH config to one per cluster
 2019-11-27 12:06:54 +01:00
Alexander Peltzer
54719c4761
Merge pull request #95 from ggabernet/master 
Update max memory for cfc profile
 2019-11-26 21:21:07 +01:00
James A. Fellows Yates
c725c71e4d
Merge branch 'master' into master 2019-11-26 20:34:42 +01:00
jfy133
6f40c13473 Split shh config for each cluster 2019-11-26 20:20:17 +01:00
phue
88b5be3060 Merge branch 'master' of https://github.com/nf-core/configs into cbe_iGenomes 2019-11-26 18:08:43 +01:00
ggabernet
834f4b4179 updated memory cfc config 2019-11-26 17:30:41 +01:00
Alexander Peltzer
ee99d7f2d4
Merge pull request #94 from apeltzer/master 
Mini Cosmetic Fixes for README
 2019-11-26 16:24:30 +01:00
Alexander Peltzer
b756ce54a4
Add genotoul fix 2019-11-26 16:09:08 +01:00
Alexander Peltzer
81739a3907
Merge pull request #93 from jfy133/master 
Updated max resources for SHH SDAG
 2019-11-26 15:56:39 +01:00
James A. Fellows Yates
c3d27099ca
Updated authors 2019-11-26 15:26:05 +01:00
James A. Fellows Yates
ca6ddcadb0
Matching max CPUs to SDAG (supercruncher8) 2019-11-26 15:25:35 +01:00
MaxUlysse
6f638b7ad4 Merge branch 'sarek' of github.com:MaxUlysse/nf-core_configs into sarek 2019-11-26 15:22:02 +01:00
MaxUlysse
25f3bd68f8 container = null 2019-11-26 15:21:53 +01:00
Alexander Peltzer
5c39c1ed1a
Merge branch 'master' into master 2019-11-26 15:07:31 +01:00
Noirot Céline
611c318569
Update conf/genotoul.config 
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
 2019-11-26 14:50:05 +01:00
Noirot Céline
dd4ff452da
Update conf/genotoul.config 
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
 2019-11-26 14:49:47 +01:00
Alexander Peltzer
37c6714cc7
Nice prince 2019-11-26 14:29:52 +01:00
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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) 
* 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