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1801 commits 4 branches 0 tags 1.9 MiB
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926 commits

Author SHA1 Message Date
Bruno Grande
80831358f9
Merge branch 'master' into bgrande/sage-aws 2022-09-01 13:21:36 -07:00
Lara Ianov
8448bb9a1e
re-define TMPDIR 2022-09-01 10:12:07 -05:00
Simon Pearce
2c738cae33
Update crukmi.config 2022-09-01 11:24:11 +01:00
Simon Pearce
a8faeda141
Update crukmi.config 2022-09-01 11:23:07 +01:00
SPearce
800931bff2 Add Sarek specific config 2022-09-01 11:13:23 +01:00
Simon Pearce
ba1d3f24cc
Update crukmi.config 2022-09-01 11:07:14 +01:00
Simon Pearce
81768e16a9
Merge branch 'nf-core:master' into crukmi 2022-09-01 10:20:25 +01:00
Simon Pearce
14a97ad0e8
Merge branch 'master' into crukmi 2022-09-01 10:07:24 +01:00
James Fellows Yates
b22e8b79c7 Fix cheaha config due to use of environmental variable 2022-09-01 11:01:23 +02:00
Kalayanee Chairat
9681716205
Update adcra.config 
Fixing typo
 2022-09-01 15:11:18 +07:00
Kalayanee Chairat
700f14d828
Merge pull request #1 from nf-core/master 
Merging from master
 2022-09-01 15:07:43 +07:00
Simon Pearce
864da0b5be
Merge branch 'master' into crukmi 2022-08-31 18:19:47 +01:00
Bruno Grande
9a37404a04
Merge branch 'master' into bgrande/sage-aws 2022-08-31 09:22:07 -07:00
Bruno Grande
179b343bd2 Incorporate resource limits 2022-08-31 09:18:27 -07:00
Bruno Grande
c883723559 Simplify resource adjustments 2022-08-31 09:10:30 -07:00
SPearce
1e1ca1e96b Incorporating executor options 2022-08-31 15:35:57 +01:00
Annick Renevey
51871ea6fc rnafusion setup for hasta usage 2022-08-31 11:32:01 +02:00
Lara Ianov
08b62ede83
Merge pull request #404 from nf-core/cheaha_singularity_update 
Cheaha Config Update
 2022-08-30 14:45:50 -05:00
James A. Fellows Yates
c70a95f9c9
Merge branch 'master' into patch-2 2022-08-29 08:23:31 +02:00
Bruno Grande
9c8cb71bc7
Merge branch 'master' into bgrande/sage-aws 2022-08-25 16:29:20 -07:00
Bruno Grande
317e5a16cb Improve AWS-related config for Sage profile 2022-08-25 16:24:52 -07:00
kalayaneech
93c4ba67a0 adding adcra configuration 2022-08-25 16:17:09 +07:00
Harshil Patel
8b9661825b Replace NC_063383.1 fasta and gff and add Nextclade config 2022-08-24 15:21:44 +01:00
Harshil Patel
8dcfcfd856 Add monkeypox genome files to viralrecon genome config file 2022-08-24 12:13:17 +01:00
Austyn Trull
8d5ae4c3ab Committing changes made by Brandon Wilk so that singularity containers will use scratch space 2022-08-23 15:30:13 -05:00
Ramprasad Neethiraj
9182b55acc
Merge branch 'master' into feat/hasta_update 2022-08-23 11:21:58 +02:00
Ramprasad Neethiraj
7ff2977a29 Merge branch 'master' of github.com:nf-core/configs into feat/hasta_update 2022-08-18 15:58:56 +02:00
Ramprasad Neethiraj
dd63dee7aa update conf 2022-08-18 15:56:41 +02:00
Ramprasad Neethiraj
1c942759ea update sentieon 2022-08-18 15:52:31 +02:00
Ramprasad Neethiraj
a6cce4ab6a
Merge branch 'master' into feat/hasta_java_memory_fix 2022-08-18 13:36:08 +02:00
SPearce
8ae3cba5e3 Reduce MPILEUP to 5GB 2022-08-15 11:35:59 +01:00
SPearce
0bfedde296 Initial attempt at a CRUKMI config file 2022-08-12 15:43:22 +01:00
Gwenna Breton
ffefefe0ab
Added contact emails 2022-08-08 16:11:55 +02:00
Gwenna Breton
6aa78833c3
Merge branch 'master' into medair 2022-08-01 16:46:55 +02:00
James A. Fellows Yates
0b47849532
Update mpcdf.config 2022-07-27 14:23:29 +02:00
Priyanka Surana
58508c4fbc Sanger profile update 2022-07-20 13:14:42 +01:00
Nicolas Vannieuwkerke
f40825ac14 lower submission rate for vsc_ugent 2022-07-14 15:50:50 +02:00
Harshil Patel
2ab126fa4d
Update default Nextclade dataset to 2022-06-14T12:00:00Z 2022-07-11 18:28:41 +01:00
Gwenna Breton
4538e8aa36
Update medair.config 
- added path to singularity image for Sentieon
- harmonized alignment
 2022-07-07 13:41:42 +02:00
qlr900
d2b6b07de8 remove comments for mnaseseq 2022-07-06 14:18:31 +02:00
Gwennid
b6e2d03a02 Added Singularity cache dir 2022-07-06 13:59:35 +02:00
qlr900
6939c6f003 lower queueSize to 5 2022-07-06 13:34:18 +02:00
qlr900
49e756d1bc fix typos 2022-07-06 12:39:55 +02:00
qlr900
56026c5ac4 remove beforeScript 2022-07-06 09:52:51 +02:00
qlr900
65d7080921 add conf/ku_sund_dangpu.config 2022-07-05 11:17:49 +02:00
James A. Fellows Yates
a141ff626b
Merge branch 'master' into eva-java-correction 2022-07-04 13:35:50 +02:00
Gwenna Breton
b3a6e199ca
Merge branch 'nf-core:master' into medair 2022-07-01 17:02:56 +02:00
Nicolas Vannieuwkerke
8a74c517d4 Merge branch 'vsc-ugent-fix' of github.com:nvnieuwk/configs into vsc-ugent-fix 2022-07-01 16:16:22 +02:00
Nicolas Vannieuwkerke
1e34595280 removed queue size limit 2022-07-01 16:16:18 +02:00
nvnieuwk
5ff845cde7
Merge branch 'master' into vsc-ugent-fix 2022-07-01 16:10:45 +02:00
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