Nicolas Vannieuwkerke
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c2b26a734d
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automated the internal cache dir location for singularity
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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
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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
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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
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2022-05-06 14:02:03 +02:00 |
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James A. Fellows Yates
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95d18270e8
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Update eva.config
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2022-05-06 13:57:11 +02:00 |
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Emil
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e938f3606f
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Removes the new SGE clusterOptions for now
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2022-05-05 14:09:45 +02:00 |
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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 |
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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 |
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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
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2022-05-03 18:30:42 +02:00 |
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Thiseas C. Lamnidis
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79e227aa4e
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Update eva.config
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2022-05-03 16:42:21 +02:00 |
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Thiseas C. Lamnidis
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085726d081
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Update eva.config
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2022-05-03 16:36:05 +02:00 |
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Thiseas C. Lamnidis
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4592969613
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memory for get_software_versions in MB.
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2022-05-03 16:30:04 +02:00 |
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Thiseas C. Lamnidis
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79ad571319
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Update eva.config
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2022-05-03 16:25:48 +02:00 |
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Thiseas C. Lamnidis
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04226692fe
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Update eva.config
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2022-05-03 16:21:35 +02:00 |
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Thiseas C. Lamnidis
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57095fe79f
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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 |
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James A. Fellows Yates
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bf658abc77
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Update eva.config
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2022-05-02 13:59:13 +02:00 |
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Alex Rajewski
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69d1a14894
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basic Cedars-Sinai HPC config file
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2022-04-22 10:17:13 -07:00 |
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James A. Fellows Yates
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c1425c6c01
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Merge pull request #364 from jfy133/eva-update
Update eager @ eva.config to allow retry on post-processing FASTQ
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2022-04-22 11:47:10 +02:00 |
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James A. Fellows Yates
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a086878c0b
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Update eva.config
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2022-04-22 10:47:04 +02:00 |
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Praveen Raj S
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edaad1cd18
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Update: sentieon version
Sentieon version has been updated to 202112.02.
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2022-04-07 12:36:01 +02:00 |
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James A. Fellows Yates
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44238471cf
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Update eva.config
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2022-03-31 13:12:50 +02:00 |
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James Fellows Yates
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2277b541a3
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Re-add bash bin specification
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2022-03-31 11:06:53 +02:00 |
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James A. Fellows Yates
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8ad4ddac6a
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Merge branch 'master' into fix-eva
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2022-03-29 12:50:54 +02:00 |
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James Fellows Yates
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3d2a612b39
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Remove setting of bash in clusterOotions
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2022-03-29 12:48:37 +02:00 |
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James A. Fellows Yates
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576351219a
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Update eva.config
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2022-03-29 12:47:46 +02:00 |
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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 |
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Mahesh Binzer-Panchal
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3a7f7f431e
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Execute sinfo with bash shell
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2022-03-25 13:58:37 +00:00 |
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Aida Andrades Valtueña
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b9da0b4f00
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Update eva.config
Update eva.config to send big memory jobs (>700G) to the bigmem queue
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2022-03-25 09:36:29 +01:00 |
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b97pla
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9a6cdfc21e
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removed process-specific requirements for sarek, request miarka high-mem node
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2022-03-24 14:25:43 +01:00 |
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b97pla
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5466d927f1
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added requirements for uppmax cluster miarka
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2022-03-23 15:29:40 +01:00 |
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James A. Fellows Yates
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962d86d604
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Merge pull request #346 from sagc-bioinformatics/sahmri
Added SAHMRI profile
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2022-03-18 13:01:36 +01:00 |
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Nathan S. Watson-Haigh
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30f710ada4
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Add debug profile
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2022-03-17 13:38:43 +10:30 |
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Praveen Raj S
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1d4f254e43
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Update munin.config
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2022-03-16 14:37:28 +01:00 |
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Praveen Raj S
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9747d5fe15
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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!
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2022-03-16 14:36:25 +01:00 |
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Alexander Peltzer
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d510cb254e
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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 |
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Praveen Raj S
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a844335942
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Update conf/munin.config
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
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2022-03-15 16:59:06 +01:00 |
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Praveen Raj S
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cb96c4bd2d
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Update conf/munin.config
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
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2022-03-15 16:56:11 +01:00 |
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Praveen Raj S
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13c66f7e98
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Update conf/munin.config
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
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2022-03-15 16:56:03 +01:00 |
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Praveen Raj S
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50c4610345
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Adjusted time and maxforks for Mutect2
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2022-03-15 16:29:19 +01:00 |
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Alexander Peltzer
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3e4fae71a4
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Merge branch 'master' into fix-show-profiles
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2022-03-15 14:52:29 +01:00 |
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James A. Fellows Yates
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1b5037ce5e
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Update eva.config
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2022-03-15 07:49:06 +01:00 |
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James A. Fellows Yates
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1565b2ce63
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Update eva.config
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2022-03-15 07:42:23 +01:00 |
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James A. Fellows Yates
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f725b6c431
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Apply suggestions from code review
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2022-03-15 07:36:34 +01:00 |
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Nathan S. Watson-Haigh
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a0f5ac7445
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Added references subdir to igenomes_base
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2022-03-15 11:41:51 +10:30 |
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James A. Fellows Yates
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4670f8bf0c
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Update eva.config
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2022-03-14 14:56:01 +01:00 |
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James A. Fellows Yates
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a2e2e94333
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Merge pull request #344 from njspix/vai
Add VAI configuration
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2022-03-14 14:36:00 +01:00 |
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Nathan Watson-Haigh
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cc55026751
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Add singularity to PATH
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2022-03-13 07:39:31 +10:30 |
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Nathan Watson-Haigh
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2f0b022571
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Fixed typos
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2022-03-13 00:08:42 +10:30 |
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Nathan Watson-Haigh
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b638694bd0
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Added SAHMRI HPC profile
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2022-03-12 21:17:33 +10:30 |
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Matiss
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6c79c75eec
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Merge pull request #290 from maxozo/master
added leicester profile
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2022-03-11 09:21:09 +00:00 |
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Nathan Spix
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d067f61329
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remove extra spaces
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2022-03-07 15:22:18 -05:00 |
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Spix
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17c77ad516
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update singularity command
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2022-03-07 15:13:26 -05:00 |
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Spix
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c97c48ae5b
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update singularity command
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2022-03-07 15:11:45 -05:00 |
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Spix
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429c7b4fa8
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initial commit
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2022-03-07 15:01:46 -05:00 |
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Alexander Peltzer
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d0d86bfb2a
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Merge pull request #339 from jfy133/rnaseq_mpcdf
Add RNASEQ specific config for MPCDF
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2022-03-07 13:59:08 +01:00 |
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James A. Fellows Yates
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975fca6721
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Apply suggestions from code review
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2022-03-07 13:51:00 +01:00 |
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Natalia Zajac
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97058995ef
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Update on singularity cache
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2022-03-07 12:37:01 +01:00 |
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Natalia Zajac
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e07a0e548e
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Config Addition
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2022-03-04 12:16:01 +01:00 |
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James Fellows Yates
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70318c3b2a
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Tweak eager settigs
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2022-03-03 14:29:30 +01:00 |
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James A. Fellows Yates
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546393ed18
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Apply suggestions from code review
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2022-03-03 14:22:35 +01:00 |
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ilight1542
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5a0543e4ac
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Merge branch 'rnaseq_mpcdf' into mpcdf_eager_config_update
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2022-03-03 14:17:18 +01:00 |
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ilight1542
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25c644abb7
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modified mpcdf configs (general + eager)
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2022-03-03 13:55:02 +01:00 |
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James Fellows Yates
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7112e74b73
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Tweak settings based on latest batch specs
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2022-03-03 13:43:40 +01:00 |
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James A. Fellows Yates
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17312604cf
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Update mpcdf.config
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2022-03-03 12:25:06 +01:00 |
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James Fellows Yates
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94f8cbcb84
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Add rnaseq pipeline specific config for MPCDF
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2022-03-03 12:20:02 +01:00 |
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James A. Fellows Yates
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5547e45ab5
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Merge branch 'master' into jfy133-patch
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2022-03-02 08:28:22 +01:00 |
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James A. Fellows Yates
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ea052a7b67
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Merge pull request #334 from jfy133/eva-update
eva: generalise custom SGE mem flag
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2022-03-01 09:23:04 +01:00 |
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James A. Fellows Yates
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a6c12d8edc
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Merge pull request #322 from U-BDS/master
Add UAB Cheaha profile
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2022-03-01 08:29:54 +01:00 |
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PCQ
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1ff92db608
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Merge branch 'nf-core:master' into master
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2022-02-28 14:50:41 +01:00 |
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James A. Fellows Yates
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89f6484325
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Merge pull request #319 from maltesemike/patch-2
Update mpcdf.config
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2022-02-28 14:06:06 +01:00 |
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James A. Fellows Yates
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46f046d477
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Update eva.config
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2022-02-28 14:00:37 +01:00 |
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James A. Fellows Yates
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d7d9951dbf
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Insert h_vmem for all nf-core pipelines
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2022-02-28 14:00:16 +01:00 |
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James A. Fellows Yates
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6210ee874c
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Update eva.config
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2022-02-28 13:57:37 +01:00 |
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Mei Wu
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dcba537d15
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picard md is single threaded
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2022-02-21 16:19:17 +01:00 |
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Maxime U. Garcia
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41e00ae8f9
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Update conf/munin.config
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2022-02-14 13:11:46 +01:00 |
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Praveen Raj S
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90936a5518
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Added: runOptions to singularity
To bind external mount directories at runtime.
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2022-02-14 12:45:20 +01:00 |
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Combiz Khozoie
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2d434c6ee5
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Merge pull request #321 from nf-core/combiz-patch-1
Imperial config updates
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2022-02-11 14:49:30 +00:00 |
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Maxime U. Garcia
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4a936a685e
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Merge pull request #317 from nf-core/praveenraj2018-patch-1
Added genome parameter
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2022-02-11 15:33:18 +01:00 |
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Combiz Khozoie
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a77f718ae2
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Merge pull request #330 from nf-core/master
Pulling master to branch
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2022-02-11 14:18:01 +00:00 |
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Combiz Khozoie
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3ce32f50c4
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Update imperial.config
Moved params configs from internal profile to universal
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2022-02-11 11:02:40 +00:00 |
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Combiz Khozoie
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b99b74b2d3
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Update imperial.config
Fixed indent
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2022-02-11 00:26:45 +00:00 |
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Combiz Khozoie
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38a05a6531
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Update imperial.config
Reworked to use internal profiles for the Imperial HPC and the MedBio cluster.
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2022-02-10 23:46:14 +00:00 |
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Combiz Khozoie
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e1d0bf0cd2
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Delete imperial_mb.config
Separate config for the medbio queue now deprecated in favour of an internal profile within the main imperial.config
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2022-02-10 23:44:49 +00:00 |
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Combiz Khozoie
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fe5474a029
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Update imperial.config
Multiple process level updates reflecting the latest job sizing guidelines for the Imperial HPC
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2022-02-10 23:02:47 +00:00 |
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Harshil Patel
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8fa6ab9b35
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Merge pull request #323 from stevin-wilson/patch-1
Added ARTIC v4.1 primer set information
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2022-02-10 19:17:47 +00:00 |
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James Fellows Yates
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88ddc9eee7
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fffff
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2022-02-10 11:34:57 +01:00 |
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James Fellows Yates
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d7d0f5cecc
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Change base time
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2022-02-10 11:32:49 +01:00 |
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James Fellows Yates
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dbd78f8075
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Re add .
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2022-02-10 11:26:18 +01:00 |
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James Fellows Yates
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dd94895f16
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remove quotes
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2022-02-10 11:22:45 +01:00 |
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James Fellows Yates
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39c2d9b25b
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Oops
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2022-02-10 11:19:16 +01:00 |
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James Fellows Yates
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c0ee3225ad
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Add times for 365d
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2022-02-10 11:02:52 +01:00 |
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