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747 commits

Author SHA1 Message Date
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 
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 
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 
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 
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 
Unibe ibu
 2021-11-19 00:56:25 +01:00
Phil Ewels
291fcb20a5
Merge pull request #297 from vsmalladi/azure 
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 
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 
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 
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 
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 
* 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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
Add auto-cleanup for MPCDF
 2021-09-09 13:41:29 +02:00
Theo Portlock
05ad3e0577
Update conf/rosalind.config 
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 
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 
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 :(" 
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 
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 
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