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
James A. Fellows Yates
192839c8be
Merge pull request #327 from nf-core/TCLamnidis-patch-2
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Removed all time limits
2022-02-10 10:22:53 +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
Patrick Hüther
8ff6f302b4
Merge pull request #320 from rbpisupati/cbe-singularity
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cbe: update config and docs
2022-02-04 10:40:16 +01:00
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
a6dd3aa0f1
cbe: update recommended nextflow version in docs
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otherwise, the new anaconda requirements will cause conflicts
2022-02-04 10:21:52 +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
phue
c3db683535
Merge branch 'master' of github.com:nf-core/configs into cbe-singularity
2022-02-04 10:14:52 +01:00
phue
b5ab4a8258
Revert "changes to cbe module loading"
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This reverts commit 7c1c4c7fa4
2022-02-04 10:13:12 +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
rbpisupati
7c1c4c7fa4
changes to cbe module loading
2022-02-02 22:42:13 +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
f876227a38
added note on screen, conda, and interactive partitions
2022-01-28 12:18:11 -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
c49abc2e61
Merge pull request #316 from drpatelh/nextclade
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Add --nextclade_dataset params
2022-01-17 17:35:31 +00:00
Harshil Patel
cd6b8e0f17
Add --nextclade_dataset params
2022-01-17 16:51:55 +00:00
Harshil Patel
a680207b55
Merge pull request #315 from drpatelh/nextclade
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Add Nextclade genome details to viralrecon genome config
2022-01-17 11:46:47 +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
4546e0f389
Merge pull request #314 from jfy133/master
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Update eager@eva to add java buffer for bbduk
2022-01-14 07:40:56 +01:00
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
bfa7e0f8d7
Merge pull request #313 from nf-core/ameynert-patch-1
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Added memory & cluster options specification for eddie sarek config
2022-01-06 10:38:13 +00:00
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
