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
Marc Trunjer Kusk Nielsen
aad70fe86d
Merge branch 'nf-core:master' into computerome
2021-09-15 11:08:48 +02:00
Marc Trunjer Kusk Nielsen
29003e13f1
Update computerome.config
2021-09-15 10:22:57 +02:00
James A. Fellows Yates
a7b1183065
Remove 1CPU for host removal fastq
2021-09-14 11:52:21 +02:00
Marc Trunjer Kusk Nielsen
86e21b378a
Update computerome.config
2021-09-13 14:26:10 +02:00
Marc Trunjer Kusk Nielsen
275288632d
Update computerome.config
2021-09-13 14:22:22 +02:00
Marc Trunjer Kusk Nielsen
366f945a40
Update computerome.config
2021-09-13 14:20:55 +02:00
Marc Trunjer Kusk Nielsen
8ebdd43898
Update computerome.config
2021-09-13 14:01:35 +02:00
Marc Trunjer Kusk Nielsen
1071eb9d2e
Update computerome.config
2021-09-13 13:38:46 +02:00
Marc Trunjer Kusk Nielsen
2e515dc861
Update computerome.config
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Don't raise an error when --project is specified
2021-09-13 13:38:25 +02:00
Marc Trunjer Kusk Nielsen
e5cba18c9b
Update computerome.config
2021-09-13 13:28:33 +02:00
Marc Trunjer Kusk Nielsen
0327ef40ea
Update computerome.config
2021-09-13 13:20:57 +02:00
Marc Trunjer Kusk Nielsen
a0ba05fd99
Update computerome.config
2021-09-13 08:36:30 +02:00
Marc Trunjer Kusk Nielsen
84f94d92c4
Update computerome.config
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Added a way to use `--project` to provide project information to the scheduler. Inspired by the uppmax config
2021-09-10 15:10:19 +02:00
Marc Trunjer Kusk Nielsen
463df26c72
Merge branch 'nf-core:master' into computerome
2021-09-10 14:47:05 +02:00
James A. Fellows Yates
7c639ac934
Bump lib merge further
2021-09-09 14:47:20 +02:00
James A. Fellows Yates
0603aba342
Remove debugging stuff
2021-09-09 13:54:01 +02:00
James A. Fellows Yates
c799784629
Merge pull request #273 from jfy133/mpcdf-fix
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Add auto-cleanup for MPCDF
2021-09-09 13:41:29 +02:00
Theo Portlock
05ad3e0577
Update conf/rosalind.config
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-09 13:37:02 +02:00
James A. Fellows Yates
d479926c7f
Update mpcdf.config
2021-09-09 13:33:56 +02:00
James A. Fellows Yates
7ec12b6736
Update eva.config
2021-09-09 13:10:05 +02:00
James A. Fellows Yates
96e26a5411
Merge pull request #272 from jfy133/eva-eager-subprofiles
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Bump additional library merge memory for eager @ EVA
2021-09-08 15:25:07 +02:00
James A. Fellows Yates
4286a3a342
Bump additional library merge memor
2021-09-08 15:16:40 +02:00
theoportlock
b240142cc3
Adds rosalind configuration
2021-09-08 14:33:39 +02:00
Rogan Grant
a7aca37bc8
Set autoMounts to true
2021-09-06 15:15:46 -05:00
Rogan Grant
b56b7b310b
Merge pull request #266 from RoganGrant/master
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Northwestern University Genomics Nodes (new add)
2021-09-06 13:26:49 -05:00
James A. Fellows Yates
39f54db097
Update container cache
2021-09-05 12:09:02 +02:00
James A. Fellows Yates
59a0901b68
Add library merge steps to have overhead
2021-09-05 12:07:53 +02:00
Rogan Grant
54298ca0f7
Merge branch 'nf-core:master' into master
2021-09-04 15:37:03 -05:00
rogangrant
a8d06ee356
Revert "Forgot a slash :("
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This reverts commit d5601fea84
.
2021-09-04 15:36:05 -05:00
Rogan Grant
d5601fea84
Forgot a slash :(
2021-09-04 15:19:32 -05:00
Rogan Grant
2c5e454d16
Updated iGenomes path for odd local structure on Quest
2021-09-04 15:13:41 -05:00
Marc Trunjer Kusk Nielsen
1bf2d436d4
Update computerome.config
2021-09-01 22:21:31 +02:00
Marc Trunjer Kusk Nielsen
e2d54cb56c
Update computerome.config
2021-09-01 22:06:56 +02:00
Marc Trunjer Kusk Nielsen
a1413ce18e
Update computerome.config
2021-09-01 21:47:48 +02:00
Marc Trunjer Kusk Nielsen
d4c71f0d8d
Update computerome.config
2021-09-01 13:22:31 +02:00
Marc Trunjer Kusk Nielsen
fdac67afbf
Create computerome.config
2021-08-31 13:58:39 +02:00
James A. Fellows Yates
94cbb031c6
Update eva.config
2021-08-30 13:29:44 +02:00
Patrick Hüther
6c4998fa8a
reduce max_memory to 1.8TB
2021-08-27 14:01:34 +02:00
James A. Fellows Yates
5fbd938bc1
Export user env too
2021-08-27 10:08:20 +02:00
James A. Fellows Yates
bcb844f896
Merge pull request #268 from jfy133/master
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Delete SHH profiles due to decommissioning
2021-08-23 14:08:13 +02:00
James Fellows Yates
59af7f0eee
Delete SHH profiles due to decommissioning
2021-08-20 10:15:39 +02:00
James A. Fellows Yates
6701354060
Add genotyping_ug to SGE fixes
2021-08-20 10:11:11 +02:00
James Fellows Yates
b0e344846d
Changes after code review from @aidaanva
2021-08-04 10:37:49 +02:00
James Fellows Yates
76fc461670
Try new strategy for SGE/JAVA bs
2021-08-04 10:14:56 +02:00
Rogan Grant
f793ffaace
Updated iGenomes location
2021-08-03 15:10:54 -05:00
James A. Fellows Yates
00491de038
Update eva.config
2021-08-03 13:54:14 +02:00
Rogan Grant
24a2949fe2
Had executor options in wrong spot :(
2021-07-28 18:05:45 -05:00
Rogan Grant
6862fb8bfd
testing ternary operatory
2021-07-28 18:01:03 -05:00
Rogan Grant
bcc69fe83c
Enable use of himem nodes
2021-07-28 17:54:51 -05:00
Rogan Grant
ac11ca5568
Remove echo used for testing
2021-07-28 16:48:08 -05:00
Rogan Grant
3dd4f16d09
Added indicator for testing
2021-07-28 14:01:12 -05:00
Rogan Grant
09ed4d54b9
Just make command a single line for simplicity
2021-07-28 13:52:26 -05:00
Rogan Grant
09e0ea2674
typo
2021-07-28 13:46:40 -05:00
Rogan Grant
e1e0810d1b
Clean up module loading script
2021-07-28 13:44:48 -05:00
Rogan Grant
e2c566ed13
Testing "automounts"
2021-07-28 13:38:06 -05:00
Rogan Grant
f104250ff4
Removed comment
2021-07-28 13:34:49 -05:00
Rogan Grant
9df267a192
Merged duplicate params
2021-07-28 13:27:17 -05:00
Rogan Grant
ff6823ec1d
removed unnecessary space
2021-07-28 13:22:52 -05:00
Rogan Grant
9957e9eea1
Version 1 of custom config with queue-switching for long jobs and module loading
2021-07-28 13:11:02 -05:00
Barry digby
70b2644c9a
.
2021-07-27 17:39:37 +01:00
Barry digby
2b6e80561a
Merge branch 'master' of https://github.com/nf-core/configs into
2021-07-27 17:13:17 +01:00
Barry digby
4f962260d0
s
2021-07-27 17:08:53 +01:00
Barry digby
04c0da5a2f
nuig confg (lugh)
2021-07-27 17:05:27 +01:00
ameynert
2112168420
Set BLASTDB_LMDB_MAP_SIZE
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This environment variable needs to be set in order to prevent memory allocation errors in the MAKEBLASTDB process.
2021-07-22 15:07:19 +01:00
ameynert
4ceb369af5
eddie.config for viralrecon pipeline
2021-07-21 12:10:43 +01:00
Maxime U. Garcia
30e058abf0
Merge branch 'master' into master_kraken
2021-07-20 09:26:56 +02:00
Harshil Patel
962dca7a46
Add ARTIC v1200 primers to genomes config for viralrecon
2021-07-12 12:24:49 +01:00
Gisela Gabernet
e2088a008d
Merge branch 'master' into master
2021-07-03 12:24:42 +02:00
ggabernet
ee2e8392ab
add aws_tower profile
2021-07-03 12:17:21 +02:00
Harshil Patel
69f63a006d
Merge pull request #254 from drpatelh/articv4
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Add ARTIC v4 primers to genomes config for viralrecon
2021-07-01 12:31:02 +01:00
Gisela Gabernet
aae0f0bf07
Merge pull request #255 from ggabernet/master
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update cfc configs
2021-07-01 10:59:25 +02:00
ggabernet
d59d099fe8
remove load module in cfc configs
2021-07-01 10:52:54 +02:00
James A. Fellows Yates
5f4b915ae8
Update eva.config
2021-06-29 11:31:00 +02:00
Harshil Patel
93cfc48afd
Add ARTIC v4 primers to genomes config
2021-06-21 21:04:16 +01:00
Edmund Miller
21e1037e0c
docs(sysbio): Add rnaseq specific docs
2021-06-17 09:18:45 -05:00
Edmund Miller
e35c5fd1d8
fix(sysbio): Add nf-core params
2021-06-17 08:32:31 -05:00