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Author SHA1 Message Date
James Fellows Yates
58dd9d49c7 Move beforeScript exports to env scope 2022-06-15 15:21:20 +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
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 A. Fellows Yates
24e165c52d
Update pipeline/mag.config 2022-06-03 12:51:47 +02:00
James A. Fellows Yates
97d57539e3
Apply suggestions from code review 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-03 12:51:20 +02:00
James Fellows Yates
5a67eba04c Add MAG @ EVA profile 2022-06-03 12:41:08 +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
Phil Ewels
123706519e
Merge pull request #377 from nvnieuwk/vsc_ugent 
Typo in VSC UGent markdown
 2022-05-20 10:55:39 +02:00
nvnieuwk
15e03bcc7b
Merge branch 'nf-core:master' into vsc_ugent 2022-05-20 10:36:51 +02:00
Nicolas Vannieuwkerke
867dcabd97 Fix type in VSC UGent 2022-05-20 10:36:07 +02:00
nvnieuwk
817f1a4aa7
Merge pull request #376 from nvnieuwk/vsc_ugent 
Added the VSC UGent profile
 2022-05-20 10:29:50 +02:00
Nicolas Vannieuwkerke
8432e4d1dc typo 2022-05-20 09:49:42 +02:00
Nicolas Vannieuwkerke
fa39478a2d prettier 2022-05-20 09:49:04 +02:00
Nicolas Vannieuwkerke
c2b26a734d automated the internal cache dir location for singularity 2022-05-20 09:48:19 +02:00
nvnieuwk
b2f7538b33
Update docs/vsc_ugent.md 
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-05-20 09:42:31 +02:00
nvnieuwk
a3583262c2
Update docs/vsc_ugent.md 
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-05-20 09:41:02 +02:00
nvnieuwk
dba85e53fa
Update docs/vsc_ugent.md 
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-05-20 09:40:55 +02:00
Nicolas Vannieuwkerke
d12fdfb40a added to the README 2022-05-20 09:37:55 +02:00
Nicolas Vannieuwkerke
6fa8cd8a6d added the profile to the test yaml 2022-05-20 09:33:43 +02:00
Nicolas Vannieuwkerke
a2d77df2ee added default scratch location to markdown file 2022-05-20 09:32:14 +02:00
Nicolas Vannieuwkerke
8621db3440 added the profile to nfcore_custom 2022-05-20 09:21:46 +02:00
Nicolas Vannieuwkerke
2f74c91145 prettier 2022-05-20 09:18:33 +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
Sofia Stamouli
44402cf28e
Merge pull request #373 from genomic-medicine-sweden/taxprofiler_hasta 
Add hasta config for taxprofiler
 2022-05-12 15:23:26 +02:00
sofstam
ca4cdcffee Fix typo 2022-05-12 15:07:30 +02:00
sofstam
b1deb0abce Update README.md 2022-05-12 14:56:52 +02:00
Sarah Guinchard
3538f8511a removed comment 2022-05-12 11:02:42 +02:00
Sarah Guinchard
84457cc655 Update documentation 2022-05-12 11:01:36 +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 A. Fellows Yates
4a50fd40e7
Merge pull request #374 from jfy133/taxprofiler 
Add taxprofiler pipeline sepcific config for EVA
 2022-05-12 10:14:41 +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
65d07a3ead
Merge pull request #372 from nf-core/TCLamnidis-patch-1 
Update eva.config
 2022-05-06 15:53:03 +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
15c938d05b
Merge pull request #370 from drpatelh/google 
Update retry strategy for preemptible instances on GCP
 2022-05-05 11:22:36 +01:00
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
a543a3ebc6
Merge pull request #369 from TCLamnidis/master 
missing bracket in eager eva.config
 2022-05-04 13:14:10 +02:00
Thiseas C. Lamnidis
209601f782
missing bracket 2022-05-04 13:08:13 +02:00