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947 commits

Author SHA1 Message Date
James Fellows Yates
3d2a612b39 Remove setting of bash in clusterOotions 2022-03-29 12:48:37 +02:00
James A. Fellows Yates
576351219a
Update eva.config 2022-03-29 12:47:46 +02:00
James A. Fellows Yates
9e502025b9
Merge pull request #358 from aidaanva/master 
Update eva.config bigmem.q
 2022-03-28 09:11:18 +02:00
Mahesh Binzer-Panchal
3a7f7f431e Execute sinfo with bash shell 2022-03-25 13:58:37 +00:00
Aida Andrades Valtueña
b9da0b4f00
Update eva.config 
Update eva.config to send big memory jobs (>700G) to the bigmem queue
 2022-03-25 09:36:29 +01:00
b97pla
9a6cdfc21e removed process-specific requirements for sarek, request miarka high-mem node 2022-03-24 14:25:43 +01:00
b97pla
5466d927f1 added requirements for uppmax cluster miarka 2022-03-23 15:29:40 +01:00
James A. Fellows Yates
962d86d604
Merge pull request #346 from sagc-bioinformatics/sahmri 
Added SAHMRI profile
 2022-03-18 13:01:36 +01:00
Nathan S. Watson-Haigh
30f710ada4
Add debug profile 2022-03-17 13:38:43 +10:30
Praveen Raj S
1d4f254e43
Update munin.config 2022-03-16 14:37:28 +01:00
Praveen Raj S
9747d5fe15
Added PileupSummariesForMutect2 in CPU limit list 
Add PileupSummariesForMutect2 to the list to run with less threads.
Changed the MaxForks to 12
Tested on an internal sample and it worked!
 2022-03-16 14:36:25 +01:00
Alexander Peltzer
d510cb254e
Merge pull request #165 from ewels/fix-show-profiles 
Set params.custom_config_base in nextflow.config
 2022-03-15 17:13:24 +01:00
Praveen Raj S
a844335942
Update conf/munin.config 
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
 2022-03-15 16:59:06 +01:00
Praveen Raj S
cb96c4bd2d
Update conf/munin.config 
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
 2022-03-15 16:56:11 +01:00
Praveen Raj S
13c66f7e98
Update conf/munin.config 
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
 2022-03-15 16:56:03 +01:00
Praveen Raj S
50c4610345
Adjusted time and maxforks for Mutect2 2022-03-15 16:29:19 +01:00
Alexander Peltzer
3e4fae71a4
Merge branch 'master' into fix-show-profiles 2022-03-15 14:52:29 +01:00
James A. Fellows Yates
1b5037ce5e
Update eva.config 2022-03-15 07:49:06 +01:00
James A. Fellows Yates
1565b2ce63
Update eva.config 2022-03-15 07:42:23 +01:00
James A. Fellows Yates
f725b6c431
Apply suggestions from code review 2022-03-15 07:36:34 +01:00
Nathan S. Watson-Haigh
a0f5ac7445
Added references subdir to igenomes_base 2022-03-15 11:41:51 +10:30
James A. Fellows Yates
4670f8bf0c
Update eva.config 2022-03-14 14:56:01 +01:00
James A. Fellows Yates
a2e2e94333
Merge pull request #344 from njspix/vai 
Add VAI configuration
 2022-03-14 14:36:00 +01:00
Nathan Watson-Haigh
cc55026751 Add singularity to PATH 2022-03-13 07:39:31 +10:30
Nathan Watson-Haigh
2f0b022571 Fixed typos 2022-03-13 00:08:42 +10:30
Nathan Watson-Haigh
b638694bd0 Added SAHMRI HPC profile 2022-03-12 21:17:33 +10:30
Matiss
6c79c75eec
Merge pull request #290 from maxozo/master 
added leicester profile
 2022-03-11 09:21:09 +00:00
Nathan Spix
d067f61329
remove extra spaces 2022-03-07 15:22:18 -05:00
Spix
17c77ad516 update singularity command 2022-03-07 15:13:26 -05:00
Spix
c97c48ae5b update singularity command 2022-03-07 15:11:45 -05:00
Spix
429c7b4fa8 initial commit 2022-03-07 15:01:46 -05:00
Alexander Peltzer
d0d86bfb2a
Merge pull request #339 from jfy133/rnaseq_mpcdf 
Add RNASEQ specific config for MPCDF
 2022-03-07 13:59:08 +01:00
James A. Fellows Yates
975fca6721
Apply suggestions from code review 2022-03-07 13:51:00 +01:00
Natalia Zajac
97058995ef Update on singularity cache 2022-03-07 12:37:01 +01:00
Natalia Zajac
e07a0e548e Config Addition 2022-03-04 12:16:01 +01:00
James Fellows Yates
70318c3b2a Tweak eager settigs 2022-03-03 14:29:30 +01:00
James A. Fellows Yates
546393ed18
Apply suggestions from code review 2022-03-03 14:22:35 +01:00
ilight1542
5a0543e4ac
Merge branch 'rnaseq_mpcdf' into mpcdf_eager_config_update 2022-03-03 14:17:18 +01:00
ilight1542
25c644abb7 modified mpcdf configs (general + eager) 2022-03-03 13:55:02 +01:00
James Fellows Yates
7112e74b73 Tweak settings based on latest batch specs 2022-03-03 13:43:40 +01:00
James A. Fellows Yates
17312604cf
Update mpcdf.config 2022-03-03 12:25:06 +01:00
James Fellows Yates
94f8cbcb84 Add rnaseq pipeline specific config for MPCDF 2022-03-03 12:20:02 +01:00
James A. Fellows Yates
5547e45ab5
Merge branch 'master' into jfy133-patch 2022-03-02 08:28:22 +01:00
James A. Fellows Yates
ea052a7b67
Merge pull request #334 from jfy133/eva-update 
eva: generalise custom SGE mem flag
 2022-03-01 09:23:04 +01:00
James A. Fellows Yates
a6c12d8edc
Merge pull request #322 from U-BDS/master 
Add UAB Cheaha profile
 2022-03-01 08:29:54 +01:00
PCQ
1ff92db608
Merge branch 'nf-core:master' into master 2022-02-28 14:50:41 +01:00
James A. Fellows Yates
89f6484325
Merge pull request #319 from maltesemike/patch-2 
Update mpcdf.config
 2022-02-28 14:06:06 +01:00
James A. Fellows Yates
46f046d477
Update eva.config 2022-02-28 14:00:37 +01:00
James A. Fellows Yates
d7d9951dbf
Insert h_vmem for all nf-core pipelines 2022-02-28 14:00:16 +01:00
James A. Fellows Yates
6210ee874c
Update eva.config 2022-02-28 13:57:37 +01:00
Mei Wu
dcba537d15 picard md is single threaded 2022-02-21 16:19:17 +01:00
Maxime U. Garcia
41e00ae8f9
Update conf/munin.config 2022-02-14 13:11:46 +01:00
Praveen Raj S
90936a5518
Added: runOptions to singularity 
To bind external mount directories at runtime.
 2022-02-14 12:45:20 +01:00
Combiz Khozoie
2d434c6ee5
Merge pull request #321 from nf-core/combiz-patch-1 
Imperial config updates
 2022-02-11 14:49:30 +00:00
Maxime U. Garcia
4a936a685e
Merge pull request #317 from nf-core/praveenraj2018-patch-1 
Added genome parameter
 2022-02-11 15:33:18 +01:00
Combiz Khozoie
a77f718ae2
Merge pull request #330 from nf-core/master 
Pulling master to branch
 2022-02-11 14:18:01 +00:00
Combiz Khozoie
3ce32f50c4
Update imperial.config 
Moved params configs from internal profile to universal
 2022-02-11 11:02:40 +00:00
Combiz Khozoie
b99b74b2d3
Update imperial.config 
Fixed indent
 2022-02-11 00:26:45 +00:00
Combiz Khozoie
38a05a6531
Update imperial.config 
Reworked to use internal profiles for the Imperial HPC and the MedBio cluster.
 2022-02-10 23:46:14 +00:00
Combiz Khozoie
e1d0bf0cd2
Delete imperial_mb.config 
Separate config for the medbio queue now deprecated in favour of an internal profile within the main imperial.config
 2022-02-10 23:44:49 +00:00
Combiz Khozoie
fe5474a029
Update imperial.config 
Multiple process level updates reflecting the latest job sizing guidelines for the Imperial HPC
 2022-02-10 23:02:47 +00:00
Harshil Patel
8fa6ab9b35
Merge pull request #323 from stevin-wilson/patch-1 
Added ARTIC v4.1 primer set information
 2022-02-10 19:17:47 +00:00
James Fellows Yates
88ddc9eee7 fffff 2022-02-10 11:34:57 +01:00
James Fellows Yates
d7d0f5cecc Change base time 2022-02-10 11:32:49 +01:00
James Fellows Yates
dbd78f8075 Re add . 2022-02-10 11:26:18 +01:00
James Fellows Yates
dd94895f16 remove quotes 2022-02-10 11:22:45 +01:00
James Fellows Yates
39c2d9b25b Oops 2022-02-10 11:19:16 +01:00
James Fellows Yates
c0ee3225ad Add times for 365d 2022-02-10 11:02:52 +01:00
Thiseas C. Lamnidis
fa4075c2a0
Removed all time limits 2022-02-10 10:00:18 +01:00
James A. Fellows Yates
64355b84d2
Merge pull request #325 from jfy133/eva-update 
Read add empty BAM exit code for qualimap 255 for eager @ EVA
 2022-02-08 11:28:36 +01:00
James A. Fellows Yates
2b06293f64
Read add empty BAM exit code for qualitmap 255 2022-02-08 11:15:17 +01:00
James A. Fellows Yates
8d286e3b69
Merge pull request #324 from jfy133/eva-update 
New attempt of workaround SGE + Java incompatibility for eager @ EVA
 2022-02-06 20:02:03 +01:00
James A. Fellows Yates
8c5a54ac9f
Update conf/pipeline/eager/eva.config 2022-02-06 19:37:53 +01:00
James A. Fellows Yates
aa525c6ebf
Allow exit code 1 retry for all java processes 2022-02-06 09:07:53 +01:00
Stevin Wilson
dbb71161c5
Added ARTIC v4.1 primer set information 2022-02-04 15:31:51 -05:00
phue
7bf6f284fa cbe: lower the threshold for switching to m queue 2022-02-04 10:33:00 +01:00
phue
49810a69b3 cbe: add gpu support 
just in case.. note that this will need --nv in containerOptions in order to mount cuda libs into the container
 2022-02-04 10:31:58 +01:00
phue
52b6f7da21 update anaconda module 
not sure why a binary distribution needs a buildenv at all, but well
 2022-02-04 10:18:59 +01:00
James A. Fellows Yates
81fe720b00
Update eva.config 2022-02-04 09:31:33 +01:00
James A. Fellows Yates
86a9042eac
Update eva.config 2022-02-04 09:25:01 +01:00
Combiz Khozoie
81a273c730
Update imperial_mb.config 
Dropped support for pqmedbio-large which is not currently available.
 2022-02-03 18:31:02 +00:00
Combiz Khozoie
2bdf5863d9
Update imperial.config 
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 
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 
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 
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 
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 
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
Kevin Brick
94d5a1b5f2
Update nihbiowulf.config 2021-12-23 15:36:38 -05:00
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
Brad Langhorst
ac4372b610 adds varskip 2021-08-03 13:46:17 -04:00
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
937538d160
Fix typo in file path 2021-07-23 10:18:24 +01:00
ameynert
238d6e5e96
Added cacheDir to singularity in eddie profile 2021-07-23 09:33:02 +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