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Author SHA1 Message Date
Gwenna Breton
4538e8aa36
Update medair.config 
- added path to singularity image for Sentieon
- harmonized alignment
 2022-07-07 13:41:42 +02:00
Gwenna Breton
746db14d47
Update medair.md 
- updated text about storing singularity images
- updated text about using profiles
 2022-07-07 11:42:46 +02:00
Gwennid
b6e2d03a02 Added Singularity cache dir 2022-07-06 13:59:35 +02:00
Gwennid
96fd2bf217 Fixed formatting 2022-07-06 11:42:05 +02:00
Gwenna Breton
1d13dd9fbc
Changed where cgg-it is mentioned 2022-07-06 11:24:03 +02:00
Gwenna Breton
235097e58e
Addressed review comments 
- removed mention of iGenomes
- clarified whom to contact for support
 2022-07-06 11:20:59 +02:00
Gwenna Breton
1d7a34b11f
Removed comment about internal doc 2022-07-06 11:17:58 +02:00
Gwenna Breton
b202ad70ac
Removed mention of specific module versions 2022-07-06 11:16:38 +02:00
James A. Fellows Yates
08435ca300
Merge pull request #382 from jfy133/eva-java-correction 
EAGER @ EVA Further Java workarounds
 2022-07-04 13:42:13 +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
Maxime U. Garcia
49e779e337
Merge pull request #394 from nvnieuwk/vsc-ugent-fix 
Vsc ugent fix for job-intensive pipelines
 2022-07-01 16:26:41 +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
84174043e4
Added details for nf-core pipelines download 2022-06-30 16:41:50 +02:00
Gwenna Breton
2398110ea5
Added info on dowloading pipelines 2022-06-30 14:24:17 +02:00
Gwenna Breton
22f73b06f9 Updated info about the different profiles 2022-06-30 12:00:05 +02:00
Gwenna Breton
77dba3256a Add profile name to test scope 2022-06-30 11:53:02 +02:00
Gwenna Breton
abccece8a3 Added medair config file to the list 2022-06-30 11:49:47 +02:00
Gwenna Breton
77017e877a Added medair configuration docs to the list 2022-06-30 11:48:34 +02:00
Gwenna Breton
f718025e79 Added doc file for medair 2022-06-30 11:43:04 +02:00
Gwenna Breton
bb35d8e5d1 Added conf file for medair 2022-06-30 11:42:36 +02:00
Maxime U. Garcia
23669d2df6
Merge pull request #393 from Sage-Bionetworks-Workflows/bgrande/sage-sarek-config 
Include `check_max()` definition for Sage configuration
 2022-06-23 21:47:17 +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
Phil Ewels
1730751d97
Merge pull request #389 from Sage-Bionetworks-Workflows/bgrande/sage-config 
[WIP] Add custom configuration for Sage Bionetworks
 2022-06-23 11:34:40 +02:00
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 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
Maxime U. Garcia
b50af6bf7e
Merge pull request #388 from nvnieuwk/singularity-fix-for-vsc_ugent 
Singularity fix for vsc ugent
 2022-06-08 16:34:38 +02:00
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
Maxime U. Garcia
5fdc8b7b1b
Merge pull request #381 from maxulysse/master 
add fix linting from comment
 2022-06-07 11:54:19 +02:00
Maxime U. Garcia
b0f1746abf
Merge branch 'master' into master 2022-06-07 11:42:50 +02:00
James A. Fellows Yates
515cbf0a77
Merge pull request #385 from nvnieuwk/fix-for-failing-tests-vsc-ugent-profile 
Fix for failing tests for vsc_ugent
 2022-06-07 11:41:00 +02:00
Nicolas Vannieuwkerke
44e25830e4 update for vsc_ugent 2022-06-07 11:33:22 +02:00