Bruno Grande
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a19d79f6ff
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Move check_max() to global config
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2022-06-23 09:44:16 -07:00 |
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Bruno Grande
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1c7230cb08
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Add Sage-specific Sarek config
|
2022-06-23 09:15:42 -07:00 |
|
Bruno Grande
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37121faf4a
|
Fix typoe with label name
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2022-06-22 14:37:43 -07:00 |
|
Bruno Grande
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ecd898584d
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Handle Sarek-specific max labels
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2022-06-22 13:54:13 -07:00 |
|
Bruno Grande
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c7093dee13
|
Reduce max_memory to fit on an instance
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2022-06-16 12:37:32 -07:00 |
|
James Fellows Yates
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acabcbd9e8
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Use _JAVA_OPTIONS instead
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2022-06-15 15:27:40 +02:00 |
|
James Fellows Yates
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76b0d1dd85
|
Merge branch 'eva-java-correction' of github.com:jfy133/nf-core-configs into eva-java-correction
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2022-06-15 15:22:25 +02:00 |
|
James Fellows Yates
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58dd9d49c7
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Move beforeScript exports to env scope
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2022-06-15 15:21:20 +02:00 |
|
Emil Bertilsson
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c8c795595a
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Merge branch 'nf-core:master' into feat/hasta_java_memory_fix
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2022-06-09 15:10:46 +02:00 |
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Emil Bertilsson
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72e995f326
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Adds generic fix for java memory issue on slurm
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2022-06-09 10:28:20 +02:00 |
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Bruno Grande
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2898736cbe
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Add Sage Bionetworks nf-core configuration
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2022-06-08 14:16:52 -07:00 |
|
Nicolas Vannieuwkerke
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b6d38859f0
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fix for singularity cache for vsc_ugent profile
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2022-06-08 16:28:28 +02:00 |
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Nicolas Vannieuwkerke
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98eacf030d
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fix for singularity cache for vsc_ugent profile
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2022-06-08 16:27:48 +02:00 |
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Andrew Frank
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d8c2775976
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Update google.config to fix custom VM memory error
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2022-06-07 09:41:41 -04:00 |
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Maxime U. Garcia
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844d250011
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Merge branch 'master' into eva-java-correction
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2022-06-07 11:57:05 +02:00 |
|
Nicolas Vannieuwkerke
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44e25830e4
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update for vsc_ugent
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2022-06-07 11:33:22 +02:00 |
|
James A. Fellows Yates
|
46fba9c597
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Update eva.config
|
2022-06-03 21:10:48 +02:00 |
|
James A. Fellows Yates
|
05cc8a08f1
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Update eva.config
|
2022-06-03 21:08:19 +02:00 |
|
Åshild J. Vågene
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ed526530d2
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Rename mjolnir_globe to mjolnir_globe.config
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2022-06-03 17:15:12 +02:00 |
|
Åshild J. Vågene
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22ed36a73d
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cacheDir update
|
2022-06-03 15:33:58 +02:00 |
|
James Fellows Yates
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9ef52af084
|
Increase overhead
|
2022-06-03 14:24:27 +02:00 |
|
James Fellows Yates
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c40ebb9acf
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Add overhead for get_software_versions
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2022-06-03 14:21:41 +02:00 |
|
James Fellows Yates
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df0429ce9d
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Replace oracle specific _JAVA_OPTIONS to portable JAVA_TOOLS_OPTIONS
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2022-06-03 14:20:39 +02:00 |
|
Phil Ewels
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b51059a3ae
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Merge branch 'master' into config_ucph-mjolnir_ash
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2022-06-03 13:21:36 +02:00 |
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James A. Fellows Yates
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7353fb257d
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Merge pull request #380 from jfy133/taxprofiler
Add MAG @ EVA profile
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2022-06-03 12:54:47 +02:00 |
|
James Fellows Yates
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5a67eba04c
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Add MAG @ EVA profile
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2022-06-03 12:41:08 +02:00 |
|
Åshild J. Vågene
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9b9a6f0188
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Update and rename holo_globe to mjolnir_globe
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2022-06-02 15:09:52 +02:00 |
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Åshild J. Vågene
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6d9cc91c5f
|
Update holo_globe
|
2022-06-02 15:03:47 +02:00 |
|
Åshild J. Vågene
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64fe4677b1
|
Update holo_globe
|
2022-05-31 15:26:23 +02:00 |
|
Åshild J. Vågene
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0b51552e88
|
Update holo_globe
|
2022-05-31 15:23:43 +02:00 |
|
Emil Bertilsson
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80e2a50a2f
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Merge pull request #378 from raysloks/feat/hasta_java_memory_fix
Feat/hasta java memory fix
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2022-05-30 14:40:52 +02:00 |
|
Emil
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8453f6b41a
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Moves qualimap arg to pipeline-specific config
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2022-05-30 12:58:12 +02:00 |
|
Emil
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29fa08c434
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Adds _JAVA_OPTIONS to singularity whitelist
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2022-05-30 11:07:24 +02:00 |
|
Emil
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19497a4183
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Makes qualimap fix work for most memory amounts
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2022-05-30 11:06:48 +02:00 |
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Åshild J. Vågene
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bb25c77e7c
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Update holo_globe
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2022-05-20 17:01:30 +02:00 |
|
Åshild J. Vågene
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d3e5c79fb4
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Create holo_globe
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2022-05-20 15:44:20 +02:00 |
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Nicolas Vannieuwkerke
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c2b26a734d
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automated the internal cache dir location for singularity
|
2022-05-20 09:48:19 +02:00 |
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Nicolas Vannieuwkerke
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cc86e6b270
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Added the VSC UGent profile
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2022-05-20 09:12:18 +02:00 |
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Sarah Guinchard
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be9711731a
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Merge pull request #375 from nf-core/ifb_core-config-update
Ifb core config update
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2022-05-13 14:45:44 +02:00 |
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Sarah Guinchard
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3538f8511a
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removed comment
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2022-05-12 11:02:42 +02:00 |
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sofstam
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54b3cda34d
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Add review suggestion
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2022-05-12 11:00:26 +02:00 |
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Sarah Guinchard
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6bb7c1a422
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Update config file with queue & correct ressources
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2022-05-12 10:55:00 +02:00 |
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sofstam
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c59149d64c
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Update docs for hasta config
|
2022-05-12 10:47:03 +02:00 |
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James Fellows Yates
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e1f780d976
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Add taxprofiler for eVA
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2022-05-12 07:54:17 +01:00 |
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sofstam
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5bc6ed90bd
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Add hasta config for taxprofiler
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2022-05-11 11:13:31 +02:00 |
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Thiseas C. Lamnidis
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d09f5fc116
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Update eva.config
eigenstrat_snp_coverage also loads pandas
|
2022-05-06 15:12:04 +02:00 |
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James A. Fellows Yates
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8fbfcfe256
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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
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20c826fd50
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Update retry strategy for preemptible instances on GCP
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2022-05-05 11:10:05 +01:00 |
|
Emil
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8b9744723c
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Fixes hasta java memory issues
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2022-05-04 14:13:24 +02:00 |
|
Thiseas C. Lamnidis
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209601f782
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missing bracket
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2022-05-04 13:08:13 +02:00 |
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Thiseas C. Lamnidis
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a42c4344ad
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Exclude bionode 06 for software versions
|
2022-05-03 18:30:42 +02:00 |
|
Thiseas C. Lamnidis
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79e227aa4e
|
Update eva.config
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2022-05-03 16:42:21 +02:00 |
|
Thiseas C. Lamnidis
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085726d081
|
Update eva.config
|
2022-05-03 16:36:05 +02:00 |
|
Thiseas C. Lamnidis
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4592969613
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memory for get_software_versions in MB.
|
2022-05-03 16:30:04 +02:00 |
|
Thiseas C. Lamnidis
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79ad571319
|
Update eva.config
|
2022-05-03 16:25:48 +02:00 |
|
Thiseas C. Lamnidis
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04226692fe
|
Update eva.config
|
2022-05-03 16:21:35 +02:00 |
|
Thiseas C. Lamnidis
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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.
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2022-05-03 16:12:20 +02:00 |
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James A. Fellows Yates
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b5d9b79377
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Merge branch 'nf-core:master' into master
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2022-05-02 13:59:18 +02:00 |
|
James A. Fellows Yates
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bf658abc77
|
Update eva.config
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2022-05-02 13:59:13 +02:00 |
|
Ramprasad Neethiraj
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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
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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
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9da85209f2
|
change bcftools output format
|
2022-04-22 11:05:56 +02:00 |
|
Ramprasad Neethiraj
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447b3ee05d
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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
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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
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44238471cf
|
Update eva.config
|
2022-03-31 13:12:50 +02:00 |
|
James Fellows Yates
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2277b541a3
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Re-add bash bin specification
|
2022-03-31 11:06:53 +02:00 |
|
James A. Fellows Yates
|
8ad4ddac6a
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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
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9e502025b9
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Merge pull request #358 from aidaanva/master
Update eva.config bigmem.q
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2022-03-28 09:11:18 +02:00 |
|
Mahesh Binzer-Panchal
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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
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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 |
|