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
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
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 A. Fellows Yates
8739aabbf0
Bump markduplicates by default
2022-02-02 08:00:13 +01:00
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
