James A. Fellows Yates
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8739aabbf0
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Bump markduplicates by default
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2022-02-02 08:00:13 +01:00 |
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James A. Fellows Yates
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5fd5c43906
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Update eva.config
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2022-01-14 07:03:05 +01:00 |
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James A. Fellows Yates
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55f452d81e
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Update eva.config
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2021-12-07 09:27:28 +01:00 |
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James Fellows Yates
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e8252ad61c
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Reintroduce bionode8, bump overhead for flagstat
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2021-12-03 08:36:31 +01:00 |
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James Fellows Yates
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06b40798c0
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Exclude bionode8
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2021-12-02 10:35:35 +01:00 |
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James A. Fellows Yates
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ffdb0a937f
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Take previous working one I think
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2021-10-18 10:58:06 +02:00 |
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James A. Fellows Yates
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b269a577e6
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Revert 1240k
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2021-10-18 10:52:28 +02:00 |
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Thiseas C. Lamnidis
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e741ecb7a7
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Update eva.config
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2021-10-13 13:04:41 +02:00 |
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Thiseas C. Lamnidis
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92648c1c1f
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added 1240k profile
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2021-10-12 15:12:49 +02:00 |
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pierrespc
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035ab61f61
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added unlimitedtime profile to maestro; changed cache for bwa process
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2021-10-08 09:05:46 +02:00 |
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pierrespc
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1621585558
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improving documentation
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2021-10-04 16:08:33 +02:00 |
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pierrespc
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e5d4a357c5
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clean doc
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2021-10-04 15:08:01 +02:00 |
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pierrespc
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f6266879d6
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edited maestronuclear and maestromitocondrial configs. The latter has not been optimized yet
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2021-09-29 13:47:35 +02:00 |
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pierrespc
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b71df6fe57
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renamed eager pipeline config file
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2021-09-29 13:22:07 +02:00 |
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pierrespc
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9ea3e2096a
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long and normal qos profiles defined now in an unique maestro config file. maestro.config also defined in pipeline/eager for ressources assignation to specific processes
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2021-09-29 13:11:14 +02:00 |
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James A. Fellows Yates
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a7b1183065
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Remove 1CPU for host removal fastq
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2021-09-14 11:52:21 +02:00 |
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James A. Fellows Yates
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7c639ac934
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Bump lib merge further
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2021-09-09 14:47:20 +02:00 |
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James A. Fellows Yates
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0603aba342
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Remove debugging stuff
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2021-09-09 13:54:01 +02:00 |
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James A. Fellows Yates
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7ec12b6736
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Update eva.config
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2021-09-09 13:10:05 +02:00 |
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James A. Fellows Yates
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4286a3a342
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Bump additional library merge memor
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2021-09-08 15:16:40 +02:00 |
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James A. Fellows Yates
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59a0901b68
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Add library merge steps to have overhead
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2021-09-05 12:07:53 +02:00 |
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James A. Fellows Yates
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94cbb031c6
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Update eva.config
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2021-08-30 13:29:44 +02:00 |
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James A. Fellows Yates
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5fbd938bc1
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Export user env too
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2021-08-27 10:08:20 +02:00 |
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James A. Fellows Yates
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bcb844f896
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Merge pull request #268 from jfy133/master
Delete SHH profiles due to decommissioning
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2021-08-23 14:08:13 +02:00 |
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James Fellows Yates
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59af7f0eee
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Delete SHH profiles due to decommissioning
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2021-08-20 10:15:39 +02:00 |
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James A. Fellows Yates
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6701354060
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Add genotyping_ug to SGE fixes
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2021-08-20 10:11:11 +02:00 |
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James Fellows Yates
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b0e344846d
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Changes after code review from @aidaanva
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2021-08-04 10:37:49 +02:00 |
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James Fellows Yates
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76fc461670
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Try new strategy for SGE/JAVA bs
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2021-08-04 10:14:56 +02:00 |
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James A. Fellows Yates
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00491de038
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Update eva.config
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2021-08-03 13:54:14 +02:00 |
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James A. Fellows Yates
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5f4b915ae8
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Update eva.config
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2021-06-29 11:31:00 +02:00 |
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James A. Fellows Yates
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756f067213
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Merge pull request #248 from jfy133/eva
Fix MakeSeqDict eager @ eva
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2021-06-07 13:26:05 +02:00 |
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James A. Fellows Yates
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da8e002969
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Merge pull request #247 from jfy133/shh-fx
Fix eageR@SHH HOPS profile human ref path
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2021-06-07 10:55:01 +02:00 |
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James A. Fellows Yates
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fc8b1162c1
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Fix HOPS huamn ref path
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2021-06-07 10:48:35 +02:00 |
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James A. Fellows Yates
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5bf57894a5
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Merge pull request #246 from jfy133/shh-update
Make eager@SHH big_data go by default to medium via run time
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2021-06-04 12:32:28 +02:00 |
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James A. Fellows Yates
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31d46cb0a9
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Make big_data go by default to medium via run time
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2021-06-04 12:22:54 +02:00 |
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James A. Fellows Yates
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3bcd55966d
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Update eva.config
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2021-05-05 11:39:33 +02:00 |
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James A. Fellows Yates
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a849fe991c
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Add additional retry allowance for silly big data in markdups
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2021-05-04 21:43:19 +02:00 |
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James A. Fellows Yates
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eacdf89e53
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Update eva.config
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2021-04-20 13:17:35 +02:00 |
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James Fellows Yates
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be1d35840d
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Add EVA and EAGER@EVA
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2021-04-06 17:48:16 +02:00 |
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James Fellows Yates
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d69af0f287
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Merging
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2021-04-06 16:42:22 +02:00 |
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James Fellows Yates
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537f52a640
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Add MPI-EVA profile
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2021-02-14 17:50:20 +01:00 |
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James A. Fellows Yates
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e32f1e46ff
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Update shh.config
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2021-02-04 08:13:16 +01:00 |
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James A. Fellows Yates
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c515a401c7
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Update shh.config
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2021-02-04 08:06:35 +01:00 |
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James A. Fellows Yates
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82fe8a04be
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Update shh.config
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2021-02-04 08:02:33 +01:00 |
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James A. Fellows Yates
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e7ac0bae13
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Update shh.config
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2021-02-04 08:00:57 +01:00 |
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James A. Fellows Yates
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eb725f9ea3
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Update shh.config
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2021-02-03 20:13:09 +01:00 |
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James A. Fellows Yates
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1c25cb033b
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Add big_data profile
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2021-01-19 13:53:01 +01:00 |
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James A. Fellows Yates
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11f1fb71db
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Update mpcdf.config
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2020-09-16 10:21:58 +02:00 |
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James A. Fellows Yates
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c6f7573d01
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Update mpcdf.config
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2020-09-15 17:48:54 +02:00 |
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James A. Fellows Yates
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bf87ec24e7
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Update mpcdf.config
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2020-09-15 17:45:38 +02:00 |
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James A. Fellows Yates
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3b7902d11b
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Mad multi-core increase CPUs on retry
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2020-09-06 08:23:35 +02:00 |
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James A. Fellows Yates
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4335e5deb7
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Update mpcdf.config
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2020-09-04 20:17:09 +02:00 |
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James A. Fellows Yates
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b4e275c3b9
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Add MPCDF for EAGER
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2020-09-04 19:57:25 +02:00 |
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James A. Fellows Yates
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5c7ab234b6
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Create mpcdf.config
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2020-09-04 19:55:40 +02:00 |
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James A. Fellows Yates
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c3fa87e4bc
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Add microbiome screening profile for NT sized MALT runs for nf-core/eager@SHH
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2020-08-11 09:18:36 +02:00 |
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James A. Fellows Yates
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57ac9257a9
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Remove now deprecated EAGER flag for HOPS profile
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2020-07-20 11:29:12 +02:00 |
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James A. Fellows Yates
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84e03b8264
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Re-bump default walltimes after debugging/testing
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2020-07-11 18:31:04 +02:00 |
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James A. Fellows Yates
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8f6409d144
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Remove min support percent value to avoid confusion
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2020-07-08 15:26:19 +02:00 |
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James A. Fellows Yates
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1af9ce293c
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Update hops profile based on requests from pathogen group
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2020-07-08 15:22:33 +02:00 |
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James A. Fellows Yates
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c57a404f18
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Add desc for hops
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2020-07-08 10:45:43 +02:00 |
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jfy133
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15dad7e2e7
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Add caveats for EAGER @ SHH profiles
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2020-07-08 09:47:03 +02:00 |
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jfy133
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926c14f7ee
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Cleverer process time submission
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2020-07-08 09:36:56 +02:00 |
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jfy133
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563c27e1bb
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Try again to get better time resource submission
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2020-07-08 09:36:28 +02:00 |
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James A. Fellows Yates
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c6905b609e
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Update shh.config
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2020-07-08 09:25:21 +02:00 |
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James A. Fellows Yates
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b360ce26bc
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Update shh.config
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2020-07-08 09:24:06 +02:00 |
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James A. Fellows Yates
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31edb4b5d7
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Update shh.config
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2020-07-08 09:20:00 +02:00 |
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James A. Fellows Yates
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aac3478e86
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Add better task time values to account for large data
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2020-07-08 09:12:11 +02:00 |
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James A. Fellows Yates
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737d826932
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Update shh.config
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2020-07-08 08:36:04 +02:00 |
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James A. Fellows Yates
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af01fccba1
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Add a HOPS profile for nf-core/eager @ SHH
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2020-07-07 14:31:11 +02:00 |
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James A. Fellows Yates
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c52428cd72
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Bump number of eager @shh retries to account for deep sequencing data
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2020-06-30 08:19:25 +02:00 |
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James A. Fellows Yates
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d070ed70d1
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Update BWA settings based on feedback
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2020-05-26 11:11:42 +02:00 |
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James A. Fellows Yates
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ff915ee504
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Update shh.config
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2020-05-12 12:47:59 +02:00 |
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James A. Fellows Yates
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cf6e697f0b
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Further update aln based on modifications of EAGER defaults
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2020-05-07 09:16:08 +02:00 |
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James A. Fellows Yates
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d42d7f4146
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Sets the bwa aln parameter to 0.01 which is more commonly used at SHH
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2020-05-04 21:02:16 +02:00 |
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James A. Fellows Yates
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638758423a
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Restricts MALT re-tries and hardcodes resources so cannot go above SDAG max
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2019-12-21 20:55:54 +01:00 |
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James A. Fellows Yates
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8747be8120
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More tweaks, nextflow appears to add a little extra?
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2019-12-06 19:27:16 +01:00 |
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James A. Fellows Yates
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5c6760b2f0
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Tweak back again
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2019-12-06 19:25:07 +01:00 |
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James A. Fellows Yates
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46f6d20a77
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Put parameters back to correct levels
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2019-12-06 19:13:29 +01:00 |
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James A. Fellows Yates
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18931763fa
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Add space?
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2019-12-06 19:11:08 +01:00 |
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James A. Fellows Yates
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f59443daf0
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Update shh.config
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2019-12-06 19:09:20 +01:00 |
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James A. Fellows Yates
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1ab1370872
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Try to make resources satisfiable
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2019-12-06 19:06:05 +01:00 |
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James A. Fellows Yates
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6e596d1730
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Fix stupid wrong bracket typo -.-
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2019-12-06 18:37:39 +01:00 |
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jfy133
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e8b4675692
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Cleanup and tweaking
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2019-12-06 13:17:31 +01:00 |
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James A. Fellows Yates
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0033b74e4e
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Update shh.config
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2019-12-05 18:08:39 +01:00 |
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James A. Fellows Yates
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dc0f1dfb40
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Update shh.config
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2019-12-05 17:58:49 +01:00 |
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James A. Fellows Yates
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b1a8b45aa0
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Maybe typo?
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2019-12-05 17:52:53 +01:00 |
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jfy133
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731372dac2
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Added SHH specific EAGER configuration
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2019-12-05 17:01:10 +01:00 |
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