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Author SHA1 Message Date
James A. Fellows Yates
8ad4ddac6a
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
9e502025b9
Merge pull request #358 from aidaanva/master 
Update eva.config bigmem.q
 2022-03-28 09:11:18 +02:00
James A. Fellows Yates
b0c9ac9be8
Update eva.md 2022-03-28 09:02:26 +02:00
Phil Ewels
1f872aea87
Merge pull request #357 from mahesh-panchal/uppmax-hostname-fix 
Execute sinfo with bash shell
 2022-03-25 15:31:09 +01:00
Mahesh Binzer-Panchal
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
Phil Ewels
7d72e8d94b
Merge pull request #356 from b97pla/uppmax_miarka_config 
removed process-specific requirements for sarek, request miarka high-…
 2022-03-24 14:33:06 +01:00
b97pla
9a6cdfc21e removed process-specific requirements for sarek, request miarka high-mem node 2022-03-24 14:25:43 +01:00
Phil Ewels
80ec4485b6
Merge pull request #355 from b97pla/uppmax_miarka_config 
added requirements for uppmax cluster miarka
 2022-03-23 16:56:44 +01:00
b97pla
5466d927f1 added requirements for uppmax cluster miarka 2022-03-23 15:29:40 +01:00
Phil Ewels
2c18f8c5da
Merge pull request #354 from Emiller88/prettier 2022-03-23 12:31:41 +01:00
Edmund Miller
590045be31
ci: Run linting only once 2022-03-21 19:23:29 -05:00
Edmund Miller
ac6c08fbf4
style: yaml => yml 2022-03-21 19:23:29 -05:00
Edmund Miller
c909b36a5e
style: Allow editorconfig to manage tab widths 2022-03-21 19:23:29 -05:00
Edmund Miller
6c37bf3b20
style: Run prettier 2022-03-21 19:23:28 -05:00
Edmund Miller
58da86d729
ci: Use prettier 2022-03-21 19:13:59 -05:00
Edmund Miller
c42ab624c2
style: Replace markdownlint with prettier 2022-03-21 19:13:56 -05:00
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
066a2181cb
Merge pull request #353 from nf-core/praveenraj2018-patch-1 
Added PileupSummariesForMutect2 in CPU limit list
 2022-03-16 14:39:43 +01:00
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
 2022-03-15 17:13:24 +01:00
Praveen Raj S
5828a48ef7
Merge pull request #351 from nf-core/praveenraj2018-patch-1 
Adjusted time and maxforks for Mutect2
 2022-03-15 17:00:09 +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
47bb41a1d8
Merge pull request #348 from jfy133/eva-update 
Update eager @ eva to exclude slow nodes for mapping
 2022-03-15 07:54:52 +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
James A. Fellows Yates
a154738c5e
Merge pull request #347 from nf-core/pr-template-update 
Update PULL_REQUEST_TEMPLATE.md
 2022-03-14 10:11:21 +01:00
James A. Fellows Yates
b7909c33c8
Update PULL_REQUEST_TEMPLATE.md 2022-03-14 08:27:10 +01:00
James A. Fellows Yates
30d9f82c65
Merge pull request #138 from Emiller88/pr-templates 
chore: add new config PR template
 2022-03-14 08:06:09 +01:00
Nathan Watson-Haigh
cc55026751 Add singularity to PATH 2022-03-13 07:39:31 +10:30
Nathan Watson-Haigh
2f0b022571 Fixed typos 2022-03-13 00:08:42 +10:30
Nathan Watson-Haigh
dba3fb4c1d Added SAHMRI HPC profile docs 2022-03-13 00:05:34 +10:30
Nathan Watson-Haigh
b58a9952be Added SAHMRI HPC profile 2022-03-12 21:24:05 +10:30
Nathan Watson-Haigh
b638694bd0 Added SAHMRI HPC profile 2022-03-12 21:17:33 +10:30
Matiss
6c79c75eec
Merge pull request #290 from maxozo/master 
added leicester profile
 2022-03-11 09:21:09 +00:00
Nathan Spix
d067f61329
remove extra spaces 2022-03-07 15:22:18 -05:00
Spix
17c77ad516 update singularity command 2022-03-07 15:13:26 -05:00
Spix
c97c48ae5b update singularity command 2022-03-07 15:11:45 -05:00