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Author SHA1 Message Date
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
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
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
Spix
429c7b4fa8 initial commit 2022-03-07 15:01:46 -05:00
Alexander Peltzer
d0d86bfb2a
Merge pull request #339 from jfy133/rnaseq_mpcdf 
Add RNASEQ specific config for MPCDF
 2022-03-07 13:59:08 +01:00
James A. Fellows Yates
975fca6721
Apply suggestions from code review 2022-03-07 13:51:00 +01:00
Alexander Peltzer
5cde6f3886
Merge pull request #342 from zajacn/master 
Update on md file
 2022-03-07 13:44:00 +01:00
Natalia Zajac
c2e0c9e6d4 Update on md file 2022-03-07 12:59:56 +01:00
Phil Ewels
098296bce8
Merge pull request #341 from zajacn/master 
Addition of FGCZ config
 2022-03-07 12:48:23 +01:00
Natalia Zajac
97058995ef Update on singularity cache 2022-03-07 12:37:01 +01:00
Natalia Zajac
e07a0e548e Config Addition 2022-03-04 12:16:01 +01:00
James Fellows Yates
70318c3b2a Tweak eager settigs 2022-03-03 14:29:30 +01:00
James A. Fellows Yates
18890fc3cf
Merge pull request #3 from ilight1542/mpcdf_eager_config_update 
modified mpcdf configs (general + eager)
 2022-03-03 14:25:58 +01:00
James A. Fellows Yates
546393ed18
Apply suggestions from code review 2022-03-03 14:22:35 +01:00
ilight1542
5a0543e4ac
Merge branch 'rnaseq_mpcdf' into mpcdf_eager_config_update 2022-03-03 14:17:18 +01:00
ilight1542
25c644abb7 modified mpcdf configs (general + eager) 2022-03-03 13:55:02 +01:00
James Fellows Yates
7112e74b73 Tweak settings based on latest batch specs 2022-03-03 13:43:40 +01:00
James Fellows Yates
008ade7ab3 Merge branch 'rnaseq_mpcdf' of github.com:jfy133/nf-core-configs into rnaseq_mpcdf 2022-03-03 12:26:18 +01:00
James Fellows Yates
e649bfbb2e Linting 2022-03-03 12:26:14 +01:00
James A. Fellows Yates
17312604cf
Update mpcdf.config 2022-03-03 12:25:06 +01:00
James Fellows Yates
94f8cbcb84 Add rnaseq pipeline specific config for MPCDF 2022-03-03 12:20:02 +01:00
James A. Fellows Yates
341ea3664e
Merge pull request #336 from jfy133/master 
Fix markdown linting from recently merged configs
 2022-03-02 08:57:20 +01:00
James A. Fellows Yates
121452afad
Linting 2022-03-02 08:51:20 +01:00
James A. Fellows Yates
15a0571eae
Fix markdown 2022-03-02 08:50:42 +01:00
James A. Fellows Yates
a412510ce8
Merge pull request #335 from jfy133/master 
Remove reference to now-decomissioned dracro @ MPCDF & clean up eager @EVA
 2022-03-02 08:47:47 +01:00
James A. Fellows Yates
adcfe22f98
Remove draco entry to MPCDF profiles due to decomissioning 2022-03-02 08:38:55 +01:00
James A. Fellows Yates
8174fe6d52
Merge pull request #2 from nf-core/jfy133-patch 
sync
 2022-03-02 08:34:31 +01:00
James A. Fellows Yates
5547e45ab5
Merge branch 'master' into jfy133-patch 2022-03-02 08:28:22 +01:00
James A. Fellows Yates
ea052a7b67
Merge pull request #334 from jfy133/eva-update 
eva: generalise custom SGE mem flag
 2022-03-01 09:23:04 +01:00
James A. Fellows Yates
a6c12d8edc
Merge pull request #322 from U-BDS/master 
Add UAB Cheaha profile
 2022-03-01 08:29:54 +01:00
Austyn Trull
00deea7442 Adding cheaha to Github Actions testing yaml. 2022-02-28 10:00:13 -06:00
James A. Fellows Yates
06aaebbad1
Merge pull request #303 from PCQuilis/patch-2 
added marvin.md link
 2022-02-28 15:03:20 +01:00