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926 commits

Author SHA1 Message Date
Nicolas Vannieuwkerke
fa949a069e added queuesize 2022-07-01 16:01:19 +02:00
Nicolas Vannieuwkerke
abfa3f47f4 lowered the job submit rate of vsc_ugent 2022-07-01 15:55:44 +02:00
Gwenna Breton
bb35d8e5d1 Added conf file for medair 2022-06-30 11:42:36 +02:00
Bruno Grande
6f0d9e6c43 Complete check_max() move to global config 2022-06-23 10:10:28 -07:00
Bruno Grande
a19d79f6ff Move check_max() to global config 2022-06-23 09:44:16 -07:00
Bruno Grande
1c7230cb08 Add Sage-specific Sarek config 2022-06-23 09:15:42 -07:00
Bruno Grande
37121faf4a Fix typoe with label name 2022-06-22 14:37:43 -07:00
Bruno Grande
ecd898584d Handle Sarek-specific max labels 2022-06-22 13:54:13 -07:00
Bruno Grande
c7093dee13 Reduce max_memory to fit on an instance 2022-06-16 12:37:32 -07:00
James A. Fellows Yates
51d057564f
Fix python related seg faults mag@eva 2022-06-15 15:40:42 +02:00
James Fellows Yates
ba8bffbdfd Use env scope instead of beforescript for mag@eva 2022-06-15 15:39:36 +02:00
James Fellows Yates
d12d98fb2e Merge branches 'master' and 'eva-java-correction' of github.com:jfy133/nf-core-configs into master 2022-06-15 15:38:35 +02:00
James Fellows Yates
acabcbd9e8 Use _JAVA_OPTIONS instead 2022-06-15 15:27:40 +02:00
James Fellows Yates
76b0d1dd85 Merge branch 'eva-java-correction' of github.com:jfy133/nf-core-configs into eva-java-correction 2022-06-15 15:22:25 +02:00
James Fellows Yates
58dd9d49c7 Move beforeScript exports to env scope 2022-06-15 15:21:20 +02:00
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
James A. Fellows Yates
975fca6721
Apply suggestions from code review 2022-03-07 13:51:00 +01:00
Natalia Zajac
97058995ef Update on singularity cache 2022-03-07 12:37:01 +01:00
Natalia Zajac
e07a0e548e Config Addition 2022-03-04 12:16:01 +01:00
James Fellows Yates
70318c3b2a Tweak eager settigs 2022-03-03 14:29:30 +01:00
James A. Fellows Yates
546393ed18
Apply suggestions from code review 2022-03-03 14:22:35 +01:00
ilight1542
5a0543e4ac
Merge branch 'rnaseq_mpcdf' into mpcdf_eager_config_update 2022-03-03 14:17:18 +01:00
ilight1542
25c644abb7 modified mpcdf configs (general + eager) 2022-03-03 13:55:02 +01:00
James Fellows Yates
7112e74b73 Tweak settings based on latest batch specs 2022-03-03 13:43:40 +01:00
James A. Fellows Yates
17312604cf
Update mpcdf.config 2022-03-03 12:25:06 +01:00
James Fellows Yates
94f8cbcb84 Add rnaseq pipeline specific config for MPCDF 2022-03-03 12:20:02 +01:00
James A. Fellows Yates
5547e45ab5
Merge branch 'master' into jfy133-patch 2022-03-02 08:28:22 +01:00
James A. Fellows Yates
ea052a7b67
Merge pull request #334 from jfy133/eva-update 
eva: generalise custom SGE mem flag
 2022-03-01 09:23:04 +01:00
James A. Fellows Yates
a6c12d8edc
Merge pull request #322 from U-BDS/master 
Add UAB Cheaha profile
 2022-03-01 08:29:54 +01:00
PCQ
1ff92db608
Merge branch 'nf-core:master' into master 2022-02-28 14:50:41 +01:00
James A. Fellows Yates
89f6484325
Merge pull request #319 from maltesemike/patch-2 
Update mpcdf.config
 2022-02-28 14:06:06 +01:00
James A. Fellows Yates
46f046d477
Update eva.config 2022-02-28 14:00:37 +01:00
James A. Fellows Yates
d7d9951dbf
Insert h_vmem for all nf-core pipelines 2022-02-28 14:00:16 +01:00
James A. Fellows Yates
6210ee874c
Update eva.config 2022-02-28 13:57:37 +01:00
Mei Wu
dcba537d15 picard md is single threaded 2022-02-21 16:19:17 +01:00
Maxime U. Garcia
41e00ae8f9
Update conf/munin.config 2022-02-14 13:11:46 +01:00
Praveen Raj S
90936a5518
Added: runOptions to singularity 
To bind external mount directories at runtime.
 2022-02-14 12:45:20 +01:00
Combiz Khozoie
2d434c6ee5
Merge pull request #321 from nf-core/combiz-patch-1 
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 
Added genome parameter
 2022-02-11 15:33:18 +01:00
Combiz Khozoie
a77f718ae2
Merge pull request #330 from nf-core/master 
Pulling master to branch
 2022-02-11 14:18:01 +00:00
Combiz Khozoie
3ce32f50c4
Update imperial.config 
Moved params configs from internal profile to universal
 2022-02-11 11:02:40 +00:00
Combiz Khozoie
b99b74b2d3
Update imperial.config 
Fixed indent
 2022-02-11 00:26:45 +00:00
Combiz Khozoie
38a05a6531
Update imperial.config 
Reworked to use internal profiles for the Imperial HPC and the MedBio cluster.
 2022-02-10 23:46:14 +00:00
Combiz Khozoie
e1d0bf0cd2
Delete imperial_mb.config 
Separate config for the medbio queue now deprecated in favour of an internal profile within the main imperial.config
 2022-02-10 23:44:49 +00:00
Combiz Khozoie
fe5474a029
Update imperial.config 
Multiple process level updates reflecting the latest job sizing guidelines for the Imperial HPC
 2022-02-10 23:02:47 +00:00
Harshil Patel
8fa6ab9b35
Merge pull request #323 from stevin-wilson/patch-1 
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