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861 commits

Author SHA1 Message Date
Emil Bertilsson
c8c795595a
Merge branch 'nf-core:master' into feat/hasta_java_memory_fix 2022-06-09 15:10:46 +02:00
Emil Bertilsson
72e995f326 Adds generic fix for java memory issue on slurm 2022-06-09 10:28:20 +02:00
Bruno Grande
2898736cbe Add Sage Bionetworks nf-core configuration 2022-06-08 14:16:52 -07:00
Nicolas Vannieuwkerke
b6d38859f0 fix for singularity cache for vsc_ugent profile 2022-06-08 16:28:28 +02:00
Nicolas Vannieuwkerke
98eacf030d fix for singularity cache for vsc_ugent profile 2022-06-08 16:27:48 +02:00
Andrew Frank
d8c2775976
Update google.config to fix custom VM memory error 2022-06-07 09:41:41 -04:00
Maxime U. Garcia
844d250011
Merge branch 'master' into eva-java-correction 2022-06-07 11:57:05 +02:00
Nicolas Vannieuwkerke
44e25830e4 update for vsc_ugent 2022-06-07 11:33:22 +02:00
James A. Fellows Yates
46fba9c597
Update eva.config 2022-06-03 21:10:48 +02:00
James A. Fellows Yates
05cc8a08f1
Update eva.config 2022-06-03 21:08:19 +02:00
Åshild J. Vågene
ed526530d2
Rename mjolnir_globe to mjolnir_globe.config 2022-06-03 17:15:12 +02:00
Åshild J. Vågene
22ed36a73d
cacheDir update 2022-06-03 15:33:58 +02:00
James Fellows Yates
9ef52af084 Increase overhead 2022-06-03 14:24:27 +02:00
James Fellows Yates
c40ebb9acf Add overhead for get_software_versions 2022-06-03 14:21:41 +02:00
James Fellows Yates
df0429ce9d Replace oracle specific _JAVA_OPTIONS to portable JAVA_TOOLS_OPTIONS 2022-06-03 14:20:39 +02:00
Phil Ewels
b51059a3ae
Merge branch 'master' into config_ucph-mjolnir_ash 2022-06-03 13:21:36 +02:00
James A. Fellows Yates
7353fb257d
Merge pull request #380 from jfy133/taxprofiler 
Add MAG @ EVA profile
 2022-06-03 12:54:47 +02:00
James Fellows Yates
5a67eba04c Add MAG @ EVA profile 2022-06-03 12:41:08 +02:00
Åshild J. Vågene
9b9a6f0188
Update and rename holo_globe to mjolnir_globe 2022-06-02 15:09:52 +02:00
Åshild J. Vågene
6d9cc91c5f
Update holo_globe 2022-06-02 15:03:47 +02:00
Åshild J. Vågene
64fe4677b1
Update holo_globe 2022-05-31 15:26:23 +02:00
Åshild J. Vågene
0b51552e88
Update holo_globe 2022-05-31 15:23:43 +02:00
Emil Bertilsson
80e2a50a2f
Merge pull request #378 from raysloks/feat/hasta_java_memory_fix 
Feat/hasta java memory fix
 2022-05-30 14:40:52 +02:00
Emil
8453f6b41a Moves qualimap arg to pipeline-specific config 2022-05-30 12:58:12 +02:00
Emil
29fa08c434 Adds _JAVA_OPTIONS to singularity whitelist 2022-05-30 11:07:24 +02:00
Emil
19497a4183 Makes qualimap fix work for most memory amounts 2022-05-30 11:06:48 +02:00
Åshild J. Vågene
bb25c77e7c
Update holo_globe 2022-05-20 17:01:30 +02:00
Åshild J. Vågene
d3e5c79fb4
Create holo_globe 2022-05-20 15:44:20 +02:00
Nicolas Vannieuwkerke
c2b26a734d automated the internal cache dir location for singularity 2022-05-20 09:48:19 +02:00
Nicolas Vannieuwkerke
cc86e6b270 Added the VSC UGent profile 2022-05-20 09:12:18 +02:00
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
Emil
e938f3606f Removes the new SGE clusterOptions for now 2022-05-05 14:09:45 +02:00
Harshil Patel
20c826fd50 Update retry strategy for preemptible instances on GCP 2022-05-05 11:10:05 +01:00
Emil
8b9744723c Fixes hasta java memory issues 2022-05-04 14:13:24 +02:00
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
Ramprasad Neethiraj
40c965c76b fix sentieon errors 2022-04-29 00:20:57 +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
Ramprasad Neethiraj
9da85209f2 change bcftools output format 2022-04-22 11:05:56 +02:00
Ramprasad Neethiraj
447b3ee05d add beforescript for sentieon 2022-04-22 11:03:09 +02:00
James A. Fellows Yates
a086878c0b
Update eva.config 2022-04-22 10:47:04 +02:00
Ramprasad Neethiraj
3e3e2be04b remove duplicate entries 2022-04-22 00:09:29 +02:00
Ramprasad Neethiraj
d39bec05dc fix typo 2022-04-19 13:21:51 +02:00
Ramprasad Neethiraj
32207a2402 update path so that the sentieon version is explicit 2022-04-19 11:42:05 +02:00
Ramprasad Neethiraj
6fad232232 sentieon env variable 2022-04-19 11:27:35 +02:00
Ramprasad Neethiraj
afe935c2d0 include stub profile 2022-04-15 15:27:41 +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
James A. Fellows Yates
a2e2e94333
Merge pull request #344 from njspix/vai 
Add VAI configuration
 2022-03-14 14:36:00 +01:00
Nathan Watson-Haigh
cc55026751 Add singularity to PATH 2022-03-13 07:39:31 +10:30
Nathan Watson-Haigh
2f0b022571 Fixed typos 2022-03-13 00:08:42 +10:30
Nathan Watson-Haigh
b638694bd0 Added SAHMRI HPC profile 2022-03-12 21:17:33 +10:30
Matiss
6c79c75eec
Merge pull request #290 from maxozo/master 
added leicester profile
 2022-03-11 09:21:09 +00:00
Nathan Spix
d067f61329
remove extra spaces 2022-03-07 15:22:18 -05:00
Spix
17c77ad516 update singularity command 2022-03-07 15:13:26 -05:00
Spix
c97c48ae5b update singularity command 2022-03-07 15:11:45 -05:00
Spix
429c7b4fa8 initial commit 2022-03-07 15:01:46 -05:00
Alexander Peltzer
d0d86bfb2a
Merge pull request #339 from jfy133/rnaseq_mpcdf 
Add RNASEQ specific config for MPCDF
 2022-03-07 13:59:08 +01:00