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
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
2b06293f64
Read add empty BAM exit code for qualitmap 255
2022-02-08 11:15:17 +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
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
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
James A. Fellows Yates
50aafc6410
Update eva.config
2022-02-03 17:03:10 +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
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
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
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
James A. Fellows Yates
73b6b74c69
Merge pull request #279 from pierrespc/master
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Added Configuration files for running in Maestro HPC at Pasteur Institute, Paris
2021-10-08 19:15:47 +02:00
pierrespc
035ab61f61
added unlimitedtime profile to maestro; changed cache for bwa process
2021-10-08 09:05:46 +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
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
Mei Wu
79a79f7d8d
added pipeline-specific config
2021-09-28 10:38:25 +02:00
James A. Fellows Yates
a7b1183065
Remove 1CPU for host removal fastq
2021-09-14 11:52:21 +02:00
James A. Fellows Yates
7c639ac934
Bump lib merge further
2021-09-09 14:47:20 +02:00