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
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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
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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
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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
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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
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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
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Added genome parameter
2022-02-11 15:33:18 +01:00
Combiz Khozoie
a77f718ae2
Merge pull request #330 from nf-core/master
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Pulling master to branch
2022-02-11 14:18:01 +00:00
Combiz Khozoie
3ce32f50c4
Update imperial.config
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Moved params configs from internal profile to universal
2022-02-11 11:02:40 +00:00
Combiz Khozoie
b99b74b2d3
Update imperial.config
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Fixed indent
2022-02-11 00:26:45 +00:00
Combiz Khozoie
38a05a6531
Update imperial.config
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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
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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
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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
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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
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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
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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
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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
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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
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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