Combiz Khozoie
81a273c730
Update imperial_mb.config
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Dropped support for pqmedbio-large which is not currently available.
2022-02-03 18:31:02 +00:00
Combiz Khozoie
2bdf5863d9
Update imperial.config
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Removed my contact details. Users can request help on the nf-core slack.
2022-02-03 18:28:11 +00:00
Combiz Khozoie
731f86e7f1
Update imperial_mb.config
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Removed my contact details. Users can request help on the nf-core slack.
2022-02-03 18:27:49 +00:00
Combiz Khozoie
453080f282
Update imperial.config
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Removed my contact details. Users can request help on the nf-core slack.
2022-02-03 18:26:30 +00:00
James A. Fellows Yates
50aafc6410
Update eva.config
2022-02-03 17:03:10 +01:00
James A. Fellows Yates
e02196d6ad
Update eva.config
2022-02-03 17:02:34 +01:00
James A. Fellows Yates
0e41349324
Update eva.config
2022-02-03 17:01:54 +01:00
Michael Borg
cc380ce9a1
Update mpcdf.config
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Added polling frequencies to the config as requested by MPCDF admin. Also updated the number of (real) cores on Raven.
2022-02-02 13:33:03 +01:00
James Fellows Yates
2562a2f563
Remove virtual free
2022-02-02 08:06:00 +01:00
James A. Fellows Yates
8739aabbf0
Bump markduplicates by default
2022-02-02 08:00:13 +01:00
Austyn Trull
1c9e1bf8a1
Fixing syntax in cheaha profile
2022-01-28 14:18:57 -06:00
Lara Ianov
9c0d550222
max_memory
increase to reflect largemem
2022-01-28 11:45:13 -06:00
Austyn Trull
06541411dd
Initial commit of cheaha profile
2022-01-28 11:37:42 -06:00
Harshil Patel
9792226f5c
Update genomes.config
2022-01-27 12:45:41 +00:00
Praveen Raj S
5c1afd56bf
Added genome parameter
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Added genome parameter to the config file
2022-01-20 22:25:31 +01:00
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
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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
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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
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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
PCQ
698555f801
Rename marvin.conf to marvin.config
2021-12-15 14:44:05 +01:00
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
PCQ
3a61adb69b
Rename Marvin.conf to marvin.conf
2021-12-13 11:38:48 +01:00
PCQ
50d90cd686
Marvin Cluster addition
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Added the config for the Marvin cluster of the Universitat Pompeu Fabra (UPF)
2021-12-10 17:11:43 +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
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Unibe ibu
2021-11-19 00:56:25 +01:00
Phil Ewels
291fcb20a5
Merge pull request #297 from vsmalladi/azure
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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
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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
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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
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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
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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
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* 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
Matiss Ozols
d45a06a681
added leicester profile
2021-10-21 19:02:13 +01:00
Matiss Ozols
e8ce4fe8df
added leicester profile
2021-10-21 18:59:17 +01:00
Matiss Ozols
f8b932ae2d
added leicester profile
2021-10-21 18:32:57 +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
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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
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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
pierrespc
035ab61f61
added unlimitedtime profile to maestro; changed cache for bwa process
2021-10-08 09:05:46 +02:00
Mahesh Binzer-Panchal
e557e94bfb
Add SNIC_TMP to config
2021-10-07 16:05:03 +02:00
FriederikeHanssen
f1756ba121
Merge branch 'nf-core:master' into cfc
2021-10-04 18:04:18 +02:00
pierrespc
1621585558
improving documentation
2021-10-04 16:08:33 +02:00
pierrespc
e5d4a357c5
clean doc
2021-10-04 15:08:01 +02:00
Falko Hofmann
0950eb3518
Merge pull request #251 from phue/cbe_singularity_workaround
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cbe: send SIGUSR2 upon job termination
2021-10-04 13:24:53 +02:00
Rike
f6e16f2872
Add check_resource to respect max_resource/max_cpus
2021-10-04 10:14:02 +02:00
pierrespc
f6266879d6
edited maestronuclear and maestromitocondrial configs. The latter has not been optimized yet
2021-09-29 13:47:35 +02:00
pierrespc
b71df6fe57
renamed eager pipeline config file
2021-09-29 13:22:07 +02:00
pierrespc
9ea3e2096a
long and normal qos profiles defined now in an unique maestro config file. maestro.config also defined in pipeline/eager for ressources assignation to specific processes
2021-09-29 13:11:14 +02:00
Bjørn Peare Bartholdy
e750a6d445
Update conf/alice.config
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-09-28 13:34:12 +02:00
Bjørn Peare Bartholdy
197bd6cfb1
Merge branch 'nf-core:master' into master
2021-09-28 12:09:50 +02:00
bbartholdy
b6ccb46383
add ALICE profile
2021-09-28 12:08:27 +02:00
Mei Wu
79a79f7d8d
added pipeline-specific config
2021-09-28 10:38:25 +02:00
Mei Wu
c2d74b290a
fix md
2021-09-27 16:25:02 +02:00
Mei Wu
a8a2027f70
Merge branch 'master' into hasta
2021-09-27 16:12:23 +02:00
Mei Wu
06fac1dcfc
initial commit
2021-09-27 16:05:32 +02:00
Mei Wu
ae0adb056f
initial commit
2021-09-27 16:05:19 +02:00
Anthony Underwood
7469e20b4e
change max_time diretcive in the correct place
2021-09-25 09:23:24 +01:00
Anthony Underwood
6a970dc4a8
update max time for long queue
2021-09-23 11:59:45 +01:00
Patrick Hüther
1cbe2759c4
fix invalid rapid qos selection
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it only applies to the c partition
2021-09-22 11:54:27 +02:00
pierrespc
3e22b85b02
maestro only for normal qos
2021-09-22 10:13:46 +02:00
Anthony Underwood
50df2105fb
update long jobs to be submitted to the long queue
2021-09-21 14:42:59 +01:00
pierrespc
3b593d46ec
merged two pasteur config files for maestro
2021-09-20 15:14:50 +02:00
Harshil Patel
5068e4806f
Merge pull request #271 from theoportlock/master
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Adds Rosalind config for KCL!
2021-09-17 13:36:19 +01:00
Harshil Patel
3b95fd9ee3
Update conf/rosalind.config
2021-09-17 13:15:09 +01:00
theoportlock
9116a09afe
Fixes formatting and ignore_params
2021-09-17 13:21:32 +02:00
pierrespc
4614ff6f45
change max mem in Normal
2021-09-16 16:50:45 +02:00
pierrespc
de2a745fde
change type in Normal name
2021-09-16 16:48:26 +02:00
pierrespc
482e7cf8de
2 config files for Maestro HPC at Pasteur Institute, Paris
2021-09-16 12:40:56 +02:00
Marc Trunjer Kusk Nielsen
a55c3c04eb
Update computerome.config
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Adding genomes and modules back into schema_ingore_params to avoid warnings about unexpected parameters.
2021-09-15 19:54:51 +02:00
Marc Trunjer Kusk Nielsen
8b29b5584e
Update computerome.config
2021-09-15 14:20:02 +02:00
Marc Trunjer Kusk Nielsen
ab8a9ad0b8
Update computerome.config
2021-09-15 13:27:23 +02:00
theoportlock
9c97220919
Merge branch 'master' of https://github.com/theoportlock/configs
2021-09-15 11:43:09 +02:00
theoportlock
3c86f8f47c
Removes the broken clusterOptions
2021-09-15 11:42:43 +02:00