James A. Fellows Yates
c52428cd72
Bump number of eager @shh retries to account for deep sequencing data
2020-06-30 08:19:25 +02:00
James A. Fellows Yates
d070ed70d1
Update BWA settings based on feedback
2020-05-26 11:11:42 +02:00
James A. Fellows Yates
e31e781f29
Remove debugging
2020-05-26 11:07:06 +02:00
James A. Fellows Yates
ff915ee504
Update shh.config
2020-05-12 12:47:59 +02:00
James A. Fellows Yates
8225e07819
Condensed base params and added names for debugging
2020-05-12 12:47:25 +02:00
James A. Fellows Yates
4814bac1c3
Fix sub-profiles
2020-05-12 12:42:42 +02:00
James A. Fellows Yates
cf6e697f0b
Further update aln based on modifications of EAGER defaults
2020-05-07 09:16:08 +02:00
James A. Fellows Yates
d42d7f4146
Sets the bwa aln parameter to 0.01 which is more commonly used at SHH
2020-05-04 21:02:16 +02:00
marcel-keller
8e3803e4d7
Update ebc.config
2020-03-09 16:57:45 +02:00
marcel-keller
c00bbe982b
Update ebc.config
2020-03-09 16:51:38 +02:00
marcel-keller
3b57519500
Update ebc.config
2020-03-09 16:48:50 +02:00
marcel-keller
de914e56ee
Create ebc.config
2020-03-09 16:08:01 +02:00
Evan Floden
d8ad376f71
Merge branch 'master' into master
2020-03-06 10:29:50 +00:00
Alexander Peltzer
59a787b179
Merge pull request #122 from marchoeppner/ccga-config
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Removing old CCGA profile from docs and linting
2020-03-06 11:17:08 +01:00
mseybold
52842de88b
Update cfc.config
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test failed, so added the the default queue
2020-03-06 10:46:37 +01:00
mseybold
8e42bbd7d0
Update cfc.config
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We just added some new HighMem nodes to the cfc, Partition/queue name is qbic, each node has 128Cores and 2TB of RAM.
The old queue (Name compute) is set to default by slurm.
Each process over 60GB of RAM or over 20cpus should run on those new nodes.
So added the queue State and adjusted the max_memory and max_cpu setting.
2020-03-06 10:25:08 +01:00
Evan Floden
8a9d3ad8a0
First commit of Google Cloud config
2020-03-06 05:47:29 +00:00
phue
e2e4dd05d3
cbe: move container cache to different filesystem
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this is a workaround for squashfs errors that occur when containers are run from beeGFS
2020-03-05 16:34:20 +01:00
James A. Fellows Yates
41a45187fa
Experiment to see if 'cleanup = true' works as expected
2020-03-03 16:47:49 +01:00
Maxime Garcia
9a8bb12020
Update conf/pipeline/sarek/uppmax.config
2020-02-27 17:22:03 +01:00
Maxime Garcia
8acbdacf03
Update conf/pipeline/sarek/uppmax.config
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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
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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
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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
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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
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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
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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
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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
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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