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771 commits

Author SHA1 Message Date
Sarah Guinchard
be9711731a
Merge pull request #375 from nf-core/ifb_core-config-update 
Ifb core config update
 2022-05-13 14:45:44 +02:00
Sarah Guinchard
3538f8511a removed comment 2022-05-12 11:02:42 +02:00
sofstam
54b3cda34d Add review suggestion 2022-05-12 11:00:26 +02:00
Sarah Guinchard
6bb7c1a422 Update config file with queue & correct ressources 2022-05-12 10:55:00 +02:00
sofstam
c59149d64c Update docs for hasta config 2022-05-12 10:47:03 +02:00
James Fellows Yates
e1f780d976 Add taxprofiler for eVA 2022-05-12 07:54:17 +01:00
sofstam
5bc6ed90bd Add hasta config for taxprofiler 2022-05-11 11:13:31 +02:00
Thiseas C. Lamnidis
d09f5fc116
Update eva.config 
eigenstrat_snp_coverage also loads pandas
 2022-05-06 15:12:04 +02:00
James A. Fellows Yates
8fbfcfe256
Merge pull request #371 from jfy133/master 
Rename custom log file for EVA
 2022-05-06 14:02:03 +02:00
James A. Fellows Yates
95d18270e8
Update eva.config 2022-05-06 13:57:11 +02:00
Harshil Patel
20c826fd50 Update retry strategy for preemptible instances on GCP 2022-05-05 11:10:05 +01:00
Thiseas C. Lamnidis
209601f782
missing bracket 2022-05-04 13:08:13 +02:00
Thiseas C. Lamnidis
a42c4344ad
Exclude bionode 06 for software versions 2022-05-03 18:30:42 +02:00
Thiseas C. Lamnidis
79e227aa4e
Update eva.config 2022-05-03 16:42:21 +02:00
Thiseas C. Lamnidis
085726d081
Update eva.config 2022-05-03 16:36:05 +02:00
Thiseas C. Lamnidis
4592969613
memory for get_software_versions in MB. 2022-05-03 16:30:04 +02:00
Thiseas C. Lamnidis
79ad571319
Update eva.config 2022-05-03 16:25:48 +02:00
Thiseas C. Lamnidis
04226692fe
Update eva.config 2022-05-03 16:21:35 +02:00
Thiseas C. Lamnidis
57095fe79f
Update eva.config 
Set max heap size for java jobs in `get_software_versions`.
Limited OpenBLAS threading for python jobs that use numpy/pandas.
 2022-05-03 16:12:20 +02:00
James A. Fellows Yates
b5d9b79377
Merge branch 'nf-core:master' into master 2022-05-02 13:59:18 +02:00
James A. Fellows Yates
bf658abc77
Update eva.config 2022-05-02 13:59:13 +02:00
Alex Rajewski
69d1a14894
basic Cedars-Sinai HPC config file 2022-04-22 10:17:13 -07:00
James A. Fellows Yates
c1425c6c01
Merge pull request #364 from jfy133/eva-update 
Update eager @ eva.config to allow retry on post-processing FASTQ
 2022-04-22 11:47:10 +02:00
James A. Fellows Yates
a086878c0b
Update eva.config 2022-04-22 10:47:04 +02:00
Praveen Raj S
edaad1cd18
Update: sentieon version 
Sentieon version has been updated to 202112.02.
 2022-04-07 12:36:01 +02:00
James A. Fellows Yates
44238471cf
Update eva.config 2022-03-31 13:12:50 +02:00
James Fellows Yates
2277b541a3 Re-add bash bin specification 2022-03-31 11:06:53 +02:00
James A. Fellows Yates
8ad4ddac6a
Merge branch 'master' into fix-eva 2022-03-29 12:50:54 +02:00
James Fellows Yates
3d2a612b39 Remove setting of bash in clusterOotions 2022-03-29 12:48:37 +02:00
James A. Fellows Yates
576351219a
Update eva.config 2022-03-29 12:47:46 +02:00
James A. Fellows Yates
9e502025b9
Merge pull request #358 from aidaanva/master 
Update eva.config bigmem.q
 2022-03-28 09:11:18 +02:00
Mahesh Binzer-Panchal
3a7f7f431e Execute sinfo with bash shell 2022-03-25 13:58:37 +00:00
Aida Andrades Valtueña
b9da0b4f00
Update eva.config 
Update eva.config to send big memory jobs (>700G) to the bigmem queue
 2022-03-25 09:36:29 +01:00
b97pla
9a6cdfc21e removed process-specific requirements for sarek, request miarka high-mem node 2022-03-24 14:25:43 +01:00
b97pla
5466d927f1 added requirements for uppmax cluster miarka 2022-03-23 15:29:40 +01:00
James A. Fellows Yates
962d86d604
Merge pull request #346 from sagc-bioinformatics/sahmri 
Added SAHMRI profile
 2022-03-18 13:01:36 +01:00
Nathan S. Watson-Haigh
30f710ada4
Add debug profile 2022-03-17 13:38:43 +10:30
Praveen Raj S
1d4f254e43
Update munin.config 2022-03-16 14:37:28 +01:00
Praveen Raj S
9747d5fe15
Added PileupSummariesForMutect2 in CPU limit list 
Add PileupSummariesForMutect2 to the list to run with less threads.
Changed the MaxForks to 12
Tested on an internal sample and it worked!
 2022-03-16 14:36:25 +01:00
Alexander Peltzer
d510cb254e
Merge pull request #165 from ewels/fix-show-profiles 
Set params.custom_config_base in nextflow.config
 2022-03-15 17:13:24 +01:00
Praveen Raj S
a844335942
Update conf/munin.config 
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
 2022-03-15 16:59:06 +01:00
Praveen Raj S
cb96c4bd2d
Update conf/munin.config 
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
 2022-03-15 16:56:11 +01:00
Praveen Raj S
13c66f7e98
Update conf/munin.config 
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
 2022-03-15 16:56:03 +01:00
Praveen Raj S
50c4610345
Adjusted time and maxforks for Mutect2 2022-03-15 16:29:19 +01:00
Alexander Peltzer
3e4fae71a4
Merge branch 'master' into fix-show-profiles 2022-03-15 14:52:29 +01:00
James A. Fellows Yates
1b5037ce5e
Update eva.config 2022-03-15 07:49:06 +01:00
James A. Fellows Yates
1565b2ce63
Update eva.config 2022-03-15 07:42:23 +01:00
James A. Fellows Yates
f725b6c431
Apply suggestions from code review 2022-03-15 07:36:34 +01:00
Nathan S. Watson-Haigh
a0f5ac7445
Added references subdir to igenomes_base 2022-03-15 11:41:51 +10:30
James A. Fellows Yates
4670f8bf0c
Update eva.config 2022-03-14 14:56:01 +01:00