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189 commits

Author SHA1 Message Date
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
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
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
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
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
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
James A. Fellows Yates
0603aba342
Remove debugging stuff 2021-09-09 13:54:01 +02:00
James A. Fellows Yates
7ec12b6736
Update eva.config 2021-09-09 13:10:05 +02:00
James A. Fellows Yates
4286a3a342
Bump additional library merge memor 2021-09-08 15:16:40 +02:00
James A. Fellows Yates
59a0901b68
Add library merge steps to have overhead 2021-09-05 12:07:53 +02:00
James A. Fellows Yates
94cbb031c6
Update eva.config 2021-08-30 13:29:44 +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
James A. Fellows Yates
00491de038
Update eva.config 2021-08-03 13:54:14 +02:00
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
Harshil Patel
962dca7a46 Add ARTIC v1200 primers to genomes config for viralrecon 2021-07-12 12:24:49 +01:00
Harshil Patel
69f63a006d
Merge pull request #254 from drpatelh/articv4
Add ARTIC v4 primers to genomes config for viralrecon
2021-07-01 12:31:02 +01:00
James A. Fellows Yates
5f4b915ae8
Update eva.config 2021-06-29 11:31:00 +02:00