pierrespc
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e5d4a357c5
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clean doc
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2021-10-04 15:08:01 +02:00 |
|
Rike
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f6e16f2872
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Add check_resource to respect max_resource/max_cpus
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2021-10-04 10:14:02 +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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Mei Wu
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79a79f7d8d
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added pipeline-specific config
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2021-09-28 10:38:25 +02:00 |
|
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 |
|
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 |
|
James A. Fellows Yates
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0603aba342
|
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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ameynert
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2112168420
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Set BLASTDB_LMDB_MAP_SIZE
This environment variable needs to be set in order to prevent memory allocation errors in the MAKEBLASTDB process.
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2021-07-22 15:07:19 +01:00 |
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ameynert
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4ceb369af5
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eddie.config for viralrecon pipeline
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2021-07-21 12:10:43 +01:00 |
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Harshil Patel
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962dca7a46
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Add ARTIC v1200 primers to genomes config for viralrecon
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2021-07-12 12:24:49 +01:00 |
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Harshil Patel
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69f63a006d
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Merge pull request #254 from drpatelh/articv4
Add ARTIC v4 primers to genomes config for viralrecon
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2021-07-01 12:31:02 +01:00 |
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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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Harshil Patel
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93cfc48afd
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Add ARTIC v4 primers to genomes config
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2021-06-21 21:04:16 +01:00 |
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Edmund Miller
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21e1037e0c
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docs(sysbio): Add rnaseq specific docs
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2021-06-17 09:18:45 -05:00 |
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Edmund Miller
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e35c5fd1d8
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fix(sysbio): Add nf-core params
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2021-06-17 08:32:31 -05:00 |
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Edmund Miller
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14a2106c63
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fix(sysbio): Move rnaseq specific things to pipeline config
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2021-06-17 08:14:48 -05:00 |
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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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MaxUlysse
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73fcc4495a
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feat: update owner of profile
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2021-05-19 20:46:52 +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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f2413553a3
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Merge pull request #240 from jfy133/shh
eager@SHH Add additional retry allowance for silly big data in markdups
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2021-05-05 10:52:58 +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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Gisela Gabernet
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4e9e5d2c67
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Merge branch 'master' into cfc_sarek
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2021-04-23 16:47:04 +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 A. Fellows Yates
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161c3a33d4
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Merge branch 'master' into eva
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2021-04-07 19:28:16 +02:00 |
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ameynert
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0ab9edde72
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Delete conf/pipeline/atacseq directory
Pipeline-specific config not supported yet by ATAC-seq pipeline
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2021-04-07 09:24:30 +01:00 |
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James A. Fellows Yates
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832edaa450
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Merge branch 'master' into eva
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2021-04-06 17:51:46 +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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ameynert
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6e201a71f4
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ATAC-seq pipeline config
Java processes with overhead memory requirements
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2021-03-30 16:31:00 +01:00 |
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ameynert
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e5f2a63079
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Java overhead processes list updated
Added all processes calling GATK for Mutect2 variant calling
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2021-03-30 16:21:53 +01:00 |
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ameynert
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adfb5366b9
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Java overhead process list updated
Added HaplotypeCaller and GenotypeGVCFs to set of processes that need Java overhead
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2021-03-30 16:15:17 +01:00 |
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ameyner2
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da8cf2f207
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Added pipeline-specific config files for rnaseq and sarek
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2021-03-24 10:46:26 +00:00 |
|
Rike
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6221b67bcf
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Give Strelka a complete compute node
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2021-03-18 11:11:02 +01:00 |
|
Rike
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b1846af9d3
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reduce mapping resource further to compute node
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2021-03-18 11:10:00 +01:00 |
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FriederikeHanssen
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67c93a4743
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Update conf/pipeline/sarek/cfc.config
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
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2021-03-18 11:06:38 +01:00 |
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Rike
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b70097e495
|
remove new line
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2021-03-17 15:46:18 +01:00 |
|
Rike
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bb124a9be8
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Reduce vc to run on compute
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2021-03-11 16:11:41 +01:00 |
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FriederikeHanssen
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79ddbe1fea
|
Add missing bracket
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2021-03-11 09:29:03 +01:00 |
|
FriederikeHanssen
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0057132e02
|
remove check_reource statement
|
2021-03-11 09:27:08 +01:00 |
|
FriederikeHanssen
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eb9012919c
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Set values for processes with max_mem/max_cpus
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2021-03-10 11:16:18 +01:00 |
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drpatelh
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01a4f8559e
|
Update links to be consistent
|
2021-02-16 13:17:16 +00:00 |
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Harshil Patel
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6ffaf922c5
|
Update genomes.config
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2021-02-16 10:28:32 +00:00 |
|
Harshil Patel
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4de0855218
|
Update genomes.config
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2021-02-15 18:48:03 +00:00 |
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drpatelh
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9d500cf679
|
Reorder params
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2021-02-15 17:02:26 +00:00 |
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drpatelh
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f283dfb2dc
|
Add ARTIC primer sets to genome config
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2021-02-15 16:58:30 +00:00 |
|
James Fellows Yates
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537f52a640
|
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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86566ddd3b
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Merge pull request #204 from jfy133/master
Add a 'big_data' profile for eager @ SHH
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2021-02-04 15:07:52 +01:00 |
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James A. Fellows Yates
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e32f1e46ff
|
Update shh.config
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2021-02-04 08:13:16 +01:00 |
|
James A. Fellows Yates
|
c515a401c7
|
Update shh.config
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2021-02-04 08:06:35 +01:00 |
|
James A. Fellows Yates
|
82fe8a04be
|
Update shh.config
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2021-02-04 08:02:33 +01:00 |
|
James A. Fellows Yates
|
e7ac0bae13
|
Update shh.config
|
2021-02-04 08:00:57 +01:00 |
|
James A. Fellows Yates
|
eb725f9ea3
|
Update shh.config
|
2021-02-03 20:13:09 +01:00 |
|
James A. Fellows Yates
|
1c25cb033b
|
Add big_data profile
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2021-01-19 13:53:01 +01:00 |
|
James A. Fellows Yates
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a4c55b3ea9
|
Fix time limit 0-9 typo
|
2021-01-06 10:44:12 +01:00 |
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Combiz Khozoie
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a61992d144
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Added institutional configs for Imperial and Imperial MEDBIO. Added institutional pipeline configs for scflow for Imperial and Imperial MEDBIO
|
2020-12-18 10:21:26 +00:00 |
|
Emelie Nilsso
|
febf38dd8e
|
Removed an old process so that only relevant processes are included
|
2020-11-26 13:38:47 +01:00 |
|
Emelie Nilsso
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d61ed01d2d
|
Updated process names according to ampliseq main.nf
|
2020-11-25 17:50:30 +01:00 |
|
Emelie Nilsso
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37e7cfae2c
|
Removed unnecessary code that was used to troubleshoot
|
2020-11-24 07:14:23 +01:00 |
|
Emelie Nilsso
|
2ea06ffab8
|
Modified uppmax and ampliseq specific config to fit with the divided preparation of the database
|
2020-11-23 21:20:36 +01:00 |
|
James A. Fellows Yates
|
804f53c58c
|
Merge pull request #178 from jfy133/master
Add Max Planck Computing and Data Facility Cobra/Raven Clusters
|
2020-10-22 13:34:11 +02:00 |
|
MaxUlysse
|
8c0cc4b9ec
|
code polishing
|
2020-09-25 09:57:50 +02:00 |
|
MaxUlysse
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81f910cc95
|
add specific BamQC config
|
2020-09-25 09:49:43 +02:00 |
|
MaxUlysse
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fbe7bd133a
|
update uppmax specific sarek config
|
2020-09-25 08:33:53 +02:00 |
|
James A. Fellows Yates
|
11f1fb71db
|
Update mpcdf.config
|
2020-09-16 10:21:58 +02:00 |
|
James A. Fellows Yates
|
c6f7573d01
|
Update mpcdf.config
|
2020-09-15 17:48:54 +02:00 |
|
James A. Fellows Yates
|
bf87ec24e7
|
Update mpcdf.config
|
2020-09-15 17:45:38 +02:00 |
|
James A. Fellows Yates
|
3b7902d11b
|
Mad multi-core increase CPUs on retry
|
2020-09-06 08:23:35 +02:00 |
|
James A. Fellows Yates
|
4335e5deb7
|
Update mpcdf.config
|
2020-09-04 20:17:09 +02:00 |
|
James A. Fellows Yates
|
b4e275c3b9
|
Add MPCDF for EAGER
|
2020-09-04 19:57:25 +02:00 |
|
James A. Fellows Yates
|
5c7ab234b6
|
Create mpcdf.config
|
2020-09-04 19:55:40 +02:00 |
|
James A. Fellows Yates
|
c3fa87e4bc
|
Add microbiome screening profile for NT sized MALT runs for nf-core/eager@SHH
|
2020-08-11 09:18:36 +02:00 |
|
James A. Fellows Yates
|
57ac9257a9
|
Remove now deprecated EAGER flag for HOPS profile
|
2020-07-20 11:29:12 +02:00 |
|
James A. Fellows Yates
|
84e03b8264
|
Re-bump default walltimes after debugging/testing
|
2020-07-11 18:31:04 +02:00 |
|
James A. Fellows Yates
|
8f6409d144
|
Remove min support percent value to avoid confusion
|
2020-07-08 15:26:19 +02:00 |
|
James A. Fellows Yates
|
1af9ce293c
|
Update hops profile based on requests from pathogen group
|
2020-07-08 15:22:33 +02:00 |
|
James A. Fellows Yates
|
c57a404f18
|
Add desc for hops
|
2020-07-08 10:45:43 +02:00 |
|
jfy133
|
15dad7e2e7
|
Add caveats for EAGER @ SHH profiles
|
2020-07-08 09:47:03 +02:00 |
|
jfy133
|
926c14f7ee
|
Cleverer process time submission
|
2020-07-08 09:36:56 +02:00 |
|
jfy133
|
563c27e1bb
|
Try again to get better time resource submission
|
2020-07-08 09:36:28 +02:00 |
|
James A. Fellows Yates
|
c6905b609e
|
Update shh.config
|
2020-07-08 09:25:21 +02:00 |
|
James A. Fellows Yates
|
b360ce26bc
|
Update shh.config
|
2020-07-08 09:24:06 +02:00 |
|
James A. Fellows Yates
|
31edb4b5d7
|
Update shh.config
|
2020-07-08 09:20:00 +02:00 |
|
James A. Fellows Yates
|
aac3478e86
|
Add better task time values to account for large data
|
2020-07-08 09:12:11 +02:00 |
|