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Author SHA1 Message Date
Alex Rajewski
766eb450be
usage notes 2022-04-22 10:23:19 -07:00
Alex Rajewski
69d1a14894
basic Cedars-Sinai HPC config file 2022-04-22 10:17:13 -07:00
James A. Fellows Yates
c1425c6c01
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
9da85209f2 change bcftools output format 2022-04-22 11:05:56 +02:00
Ramprasad Neethiraj
447b3ee05d 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
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
Maxime U. Garcia
e9d93d62e0
Merge pull request #362 from nf-core/praveenraj2018-patch-1 
Update: sentieon version
 2022-04-07 12:52:33 +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
d49b21efdc
Merge pull request #361 from jfy133/master 
Re-add accidently removed BWA bionode exclusions EAGER @ EVA
 2022-03-31 14:11:54 +02:00
James A. Fellows Yates
44238471cf
Update eva.config 2022-03-31 13:12:50 +02:00
James A. Fellows Yates
f172cce8b2
Merge pull request #360 from jfy133/master 
Re-add bash bin specification for EVA
 2022-03-31 12:58:06 +02:00
James Fellows Yates
2277b541a3 Re-add bash bin specification 2022-03-31 11:06:53 +02:00
James A. Fellows Yates
7cad02d327
Merge pull request #359 from jfy133/fix-eva 
Remove -S /bin/bash in clusteroptions for EVA
 2022-03-29 13:51:41 +02:00
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
ajodeh-juma
188c3a39cc add gis.md documentation 2022-03-16 16:17:54 +03:00
ajodeh-juma
06854c9f2d add gis.md documentation 2022-03-16 15:34:36 +03:00
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