rbpisupati
9b5ac5c89d
added anaconda module for cbe
2021-01-15 12:55:46 +01:00
James A. Fellows Yates
a4c55b3ea9
Fix time limit 0-9 typo
2021-01-06 10:44:12 +01:00
Combiz Khozoie
17cf4e3b35
fixed indents
2020-12-18 15:34:56 +00:00
Combiz Khozoie
3824403b4e
removed workDir from Imperial configs
2020-12-18 10:31:36 +00:00
Combiz Khozoie
a61992d144
Added institutional configs for Imperial and Imperial MEDBIO. Added institutional pipeline configs for scflow for Imperial and Imperial MEDBIO
2020-12-18 10:21:26 +00:00
marcel-keller
c9ceaff3b3
change of directory for conda environments
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change of directory due to recent changes in our infrastructure
2020-12-09 15:11:21 +02:00
emnilsson
8cc2fc5ecb
Merge pull request #193 from emnilsson/master
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Modified ampliseq-specific uppmax-config
2020-12-02 13:40:43 +01:00
Alexander Peltzer
99985c658f
Merge pull request #194 from marcel-keller/ebc
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Update ebc.config
2020-11-26 14:12:33 +01:00
marcel-keller
5590a9743a
Update ebc.config
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queueSize to 64
2020-11-26 15:05:25 +02:00
Emelie Nilsso
febf38dd8e
Removed an old process so that only relevant processes are included
2020-11-26 13:38:47 +01:00
Emelie Nilsso
d61ed01d2d
Updated process names according to ampliseq main.nf
2020-11-25 17:50:30 +01:00
Emelie Nilsso
37e7cfae2c
Removed unnecessary code that was used to troubleshoot
2020-11-24 07:14:23 +01:00
Emelie Nilsso
cd59bba83e
Merge branch 'master' of https://github.com/nf-core/configs
2020-11-24 07:10:05 +01:00
Emelie Nilsso
c47088cda2
Merge remote-tracking branch 'origin'
2020-11-23 21:34:08 +01:00
Emelie Nilsso
2ea06ffab8
Modified uppmax and ampliseq specific config to fit with the divided preparation of the database
2020-11-23 21:20:36 +01:00
Thiseas C. Lamnidis
71d1ff2226
Add params block to sdag queue
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2020-11-18 13:04:46 +01:00
Thiseas C. Lamnidis
da781907f2
Move sdag queue specification block in sdag profile
2020-11-17 19:45:06 +01:00
Maxime Borry
c95fd9d52f
Merge pull request #186 from jfy133/shh-singularity-runoptions
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Remove custom singularity runOptions from SHH config
2020-11-10 15:39:40 +01:00
James A. Fellows Yates
9d4d682867
Update shh.config
2020-11-10 15:14:03 +01:00
Gisela Gabernet Garriga
885f0ce5f6
awsbatch config update
2020-11-09 22:41:38 +01:00
lecorguille
90d1f9072b
Add ABiMS - autoMounts = false
2020-10-22 18:18:55 +02:00
lecorguille
a63ca751ee
Add ABiMS
2020-10-22 16:57:41 +02:00
James A. Fellows Yates
804f53c58c
Merge pull request #178 from jfy133/master
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Add Max Planck Computing and Data Facility Cobra/Raven Clusters
2020-10-22 13:34:11 +02:00
James A. Fellows Yates
3995057d7f
Update mpcdf.config
2020-10-22 10:42:46 +02:00
James A. Fellows Yates
05deeca2d6
Update mpcdf.config
2020-10-15 14:22:35 +02:00
James A. Fellows Yates
e26c22b2f1
Update shh.config
2020-09-29 14:03:35 +02:00
MaxUlysse
2ccbdd3367
update params to latest version
2020-09-28 13:59:42 +02:00
MaxUlysse
8c0cc4b9ec
code polishing
2020-09-25 09:57:50 +02:00
MaxUlysse
81f910cc95
add specific BamQC config
2020-09-25 09:49:43 +02:00
MaxUlysse
fbe7bd133a
update uppmax specific sarek config
2020-09-25 08:33:53 +02:00
James A. Fellows Yates
11f1fb71db
Update mpcdf.config
2020-09-16 10:21:58 +02:00
James A. Fellows Yates
bbbdd3cb0f
Update mpcdf.config
2020-09-16 10:21:42 +02:00
James A. Fellows Yates
5b3492d240
Update mpcdf.config
2020-09-16 10:21:26 +02:00
James A. Fellows Yates
3115963b3e
Update mpcdf.config
2020-09-15 19:53:27 +02:00
James A. Fellows Yates
c6f7573d01
Update mpcdf.config
2020-09-15 17:48:54 +02:00
James A. Fellows Yates
bf87ec24e7
Update mpcdf.config
2020-09-15 17:45:38 +02:00
Edmund Miller
2c06019d89
fix(utd): Add check for less than 12 cpu
2020-09-13 20:46:14 -05:00
Edmund Miller
dc2735207e
feat(utd): add Kim queue
2020-09-13 20:46:10 -05:00
James A. Fellows Yates
3b7902d11b
Mad multi-core increase CPUs on retry
2020-09-06 08:23:35 +02:00
James A. Fellows Yates
4335e5deb7
Update mpcdf.config
2020-09-04 20:17:09 +02:00
James A. Fellows Yates
b4e275c3b9
Add MPCDF for EAGER
2020-09-04 19:57:25 +02:00
James A. Fellows Yates
5c7ab234b6
Create mpcdf.config
2020-09-04 19:55:40 +02:00
James A. Fellows Yates
0a685c1cc2
Update mpcdf.config
2020-09-03 20:24:11 +02:00
James A. Fellows Yates
42a1a15970
Create mpcdf.config
2020-09-03 20:11:56 +02:00
James A. Fellows Yates
c3fa87e4bc
Add microbiome screening profile for NT sized MALT runs for nf-core/eager@SHH
2020-08-11 09:18:36 +02:00
drpatelh
b804076959
Remove hard Singularity version
2020-08-03 11:38:10 +01:00
maxibor
69a0bd572b
add temporary CDAG setting for SHH config
2020-07-23 15:38:28 +02:00
James A. Fellows Yates
d38ffc289b
Merge pull request #173 from jfy133/shh-eager-hops-update
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Remove now deprecated EAGER flag for HOPS profile
2020-07-20 11:34:49 +02:00
James A. Fellows Yates
57ac9257a9
Remove now deprecated EAGER flag for HOPS profile
2020-07-20 11:29:12 +02:00
Alexander Peltzer
a498e98342
Merge pull request #170 from jfy133/master
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Make walltimes more sophisticated and add a HOPS profile for nf-core/eager @ SHH
2020-07-15 15:11:24 +02:00
James A. Fellows Yates
84e03b8264
Re-bump default walltimes after debugging/testing
2020-07-11 18:31:04 +02:00
James A. Fellows Yates
8f6409d144
Remove min support percent value to avoid confusion
2020-07-08 15:26:19 +02:00
James A. Fellows Yates
1af9ce293c
Update hops profile based on requests from pathogen group
2020-07-08 15:22:33 +02:00
James A. Fellows Yates
c57a404f18
Add desc for hops
2020-07-08 10:45:43 +02:00
jfy133
15dad7e2e7
Add caveats for EAGER @ SHH profiles
2020-07-08 09:47:03 +02:00
jfy133
926c14f7ee
Cleverer process time submission
2020-07-08 09:36:56 +02:00
jfy133
563c27e1bb
Try again to get better time resource submission
2020-07-08 09:36:28 +02:00
James A. Fellows Yates
c6905b609e
Update shh.config
2020-07-08 09:25:21 +02:00
James A. Fellows Yates
b360ce26bc
Update shh.config
2020-07-08 09:24:06 +02:00
James A. Fellows Yates
31edb4b5d7
Update shh.config
2020-07-08 09:20:00 +02:00
James A. Fellows Yates
aac3478e86
Add better task time values to account for large data
2020-07-08 09:12:11 +02:00
James A. Fellows Yates
737d826932
Update shh.config
2020-07-08 08:36:04 +02:00
piotr-faba-ardigen
ba24f1a1c8
Merge pull request #168 from piotr-faba-ardigen/add_bi_config
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Fix bi config
2020-07-07 14:56:43 +02:00
James A. Fellows Yates
fcdbeaa446
Merge branch 'master' into master
2020-07-07 14:34:10 +02:00
James A. Fellows Yates
af01fccba1
Add a HOPS profile for nf-core/eager @ SHH
2020-07-07 14:31:11 +02:00
Piotr Faba
cb7a6f756a
reduce complexity
2020-07-07 13:48:28 +02:00
James A. Fellows Yates
5517d2cbe0
Remove default non-profile bwa parameters from eager profile
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I realised today this is dangerous as these would not necessarily be reported if a user doesn't understand the profiles. Therefore removing these so nf-core/eager defaults are always used unless a specific profile (which would be described in the command itself) is explicitly named.
2020-07-07 13:29:13 +02:00
Piotr Faba
4181184f58
fix spaces
2020-07-02 22:00:37 +02:00
Piotr Faba
4828e78708
fix error introduced earlier
2020-07-02 21:57:44 +02:00
James A. Fellows Yates
530da4d8c0
Merge pull request #167 from jfy133/master
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Bump number of eager @shh retries to account for deep sequencing data
2020-06-30 11:33:29 +02:00
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
Adrian
e375ad97ad
reverting autoMounts due to bug
2020-06-26 13:39:37 +01:00
Phil Ewels
cd9fbb22dc
Merge pull request #161 from ewels/uct_hpc
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Update UCT hex -> hpc
2020-06-22 09:18:43 +02:00
Alexander Peltzer
7774a6a8f3
Merge pull request #163 from piotr-faba-ardigen/add_bi_config
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resolve #162 bug
2020-06-19 08:57:44 +02:00
Piotr Faba
cb26bef3f3
resolve #162 bug
2020-06-18 20:30:05 +02:00
Phil Ewels
53e118210f
Copy over HPC config
2020-06-17 15:20:22 +02:00
Phil Ewels
dbfcd7c5e9
Rename uct_hex > uct_hpc
2020-06-17 15:17:22 +02:00
Phil Ewels
17824d2d62
Merge czbiohub_aws_highpriority profile into czbiohub_aws
2020-06-16 15:20:39 +02:00
phue
6d356cc918
CBE: don't load singularity module
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singularity is now installed from CentOS repos, the environment module will be removed
2020-06-05 12:07:26 +02:00
Alexander Peltzer
f877644059
Merge branch 'master' into master
2020-05-29 11:43:47 +02:00
Alexander Peltzer
32ec230098
Merge pull request #156 from piotr-faba-ardigen/add_bi_config
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Add bi config
2020-05-27 21:03:15 +02:00
Piotr Faba
f139750bf4
print the error message before throwing Exception
2020-05-27 19:14:43 +02:00
Piotr Faba
3c695ba71c
test error display
2020-05-27 18:00:47 +02:00
Alexander Peltzer
6011419454
Merge pull request #154 from jfy133/master
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Update SHH nf-core/eager group-specific profiles
2020-05-27 17:52:09 +02:00
Piotr Faba
18d8edb046
add description and profile
2020-05-27 17:41:19 +02:00
Piotr Faba
66f191a1cf
declate NXF_GLOBAL_CONFIG in ci
2020-05-27 16:30:00 +02:00
Piotr Faba
2685275952
switch include off
2020-05-27 16:24:47 +02:00
Piotr Faba
c31b03108c
retry without Exception
2020-05-27 16:22:56 +02:00
Piotr Faba
1354ae4063
add bi config
2020-05-27 16:19:15 +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
Harshil Patel
5981e5ec27
Merge pull request #153 from FriederikeHanssen/cfc_scratch
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Add scratch = true to avoid writing of intermediate file to /tmp
2020-05-22 15:48:00 +01:00
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
38e9e54932
Merge pull request #151 from jfy133/master
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Add additional custom nf-core/eager params for SHH profile
2020-05-07 09:25:02 +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
FriederikeHanssen
d6813d9c39
Add scratch = true to avoid writing of intermediate file to /tmp
2020-05-04 17:09:43 +02:00
MaxUlysse
e6f4d58fa6
update rnafusion munin specific config
2020-04-28 17:06:04 +02:00
Adrian
ad12bd4ad1
testing automounts
2020-04-28 16:03:06 +01:00
Harshil Patel
2300d5a962
Update genomes.config
2020-04-09 18:22:41 +01:00
MaxUlysse
50a44d037b
better docs and organisation of giles
2020-04-09 17:02:36 +02:00
Maxime Garcia
34dc18faf6
Update uppmax.config
2020-04-09 11:35:37 +02:00
Adrian Larkeryd
405801638a
icr_davros sarek config description
2020-04-08 11:56:17 +01:00
Adrian Larkeryd
78be4b358e
icr_davros igenomes base
2020-04-08 11:55:16 +01:00
Maxime Garcia
d1ff87a416
Merge pull request #145 from bioatlas/master
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Adding UPPMAX specific config for ampliseq
2020-03-31 15:46:21 +02:00
Daniel Lundin
c8de9be701
Adding UPPMAX specific config for ampliseq
2020-03-31 15:17:24 +02:00
MaxUlysse
db2dd4458b
Merge remote-tracking branch 'upstream/master' into UPPMAX
2020-03-30 16:41:08 +02:00
MaxUlysse
8b570507cd
update s
2020-03-30 16:40:11 +02:00
ggabernet
c81f693f73
add cfc_dev config
2020-03-23 17:16:34 +01:00
Olga Botvinnik
52369ba6ad
Add AaegL5.0 config
2020-03-17 16:45:20 -07:00
Maxime Garcia
123132d89a
Update munin.config
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fix typo
2020-03-12 17:23:55 +01:00
Phil Ewels
5a3bdcca5b
Merge pull request #139 from Emiller88/utd
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fix(ganymede): use singularity/2.4.5
2020-03-11 16:54:01 +00:00
Maxime Garcia
b6d52fdb89
Update conf/pipeline/sarek/munin.config
2020-03-11 15:48:29 +01:00
Maxime Garcia
0f34d757a9
Update munin.config
2020-03-11 15:48:17 +01:00
MaxUlysse
d24a296a01
add munin/rnafusion specific config
2020-03-11 14:02:01 +01:00
MaxUlysse
dd1ddf864b
update sarek munin config
2020-03-11 14:01:28 +01:00
Edmund Miller
cece853663
fix(ganymede): use singularity/2.4.5
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Our 3.2.1 doesn't work right with snakemake or nextflow
2020-03-10 21:03:24 -05:00
Edmund Miller
c42bb07981
fix: Singularity => singularity
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For some reason ours are lowercase
2020-03-10 09:55:17 -05:00
Edmund Miller
123c44c56d
feat: add initial ganymede config
2020-03-09 16:18:41 -05:00
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
Adrian Larkeryd
a67e77bb57
put comments back in correct format
2020-03-05 10:42:18 +00:00
Adrian Larkeryd
46223a3dbb
remove comments
2020-03-05 10:39:19 +00:00
Adrian Larkeryd
ead67d1e90
description and contact
2020-03-05 09:24:10 +00:00
Adrian Larkeryd
a882b6cbaa
adding icr_davros config files generic and sarek
2020-03-04 15:00:33 +00:00
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
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
2019-11-26 14:50:05 +01:00
Noirot Céline
dd4ff452da
Update conf/genotoul.config
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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
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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
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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
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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
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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
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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