millironx/nf-configs
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Author SHA1 Message Date
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
James A. Fellows Yates
4fbebac9b3
Merge pull request #304 from PCQuilis/patch-1 
Create marvin.md added marvin config
 2022-02-28 15:03:07 +01:00
James A. Fellows Yates
d6f5209afc
Update marvin.md 2022-02-28 15:01:12 +01:00
James A. Fellows Yates
faf83eaeaa
Merge pull request #305 from PCQuilis/master 
conf file in lowercase
 2022-02-28 14:59:22 +01:00
James A. Fellows Yates
04d8a02ec9
Update nfcore_custom.config 2022-02-28 14:56:37 +01:00
James A. Fellows Yates
5c686f996f
Update main.yml 2022-02-28 14:52:32 +01:00
PCQ
1ff92db608
Merge branch 'nf-core:master' into master 2022-02-28 14:50:41 +01:00
James A. Fellows Yates
89f6484325
Merge pull request #319 from maltesemike/patch-2 
Update mpcdf.config
 2022-02-28 14:06:06 +01:00
James A. Fellows Yates
46f046d477
Update eva.config 2022-02-28 14:00:37 +01:00
James A. Fellows Yates
d7d9951dbf
Insert h_vmem for all nf-core pipelines 2022-02-28 14:00:16 +01:00
James A. Fellows Yates
6210ee874c
Update eva.config 2022-02-28 13:57:37 +01:00
Mei Wu
ff5750936d
Merge pull request #332 from projectoriented/hasta/markdupe_remove_cpus 
picard md is single threaded
 2022-02-23 16:40:57 +01:00
Mei Wu
dcba537d15 picard md is single threaded 2022-02-21 16:19:17 +01:00
Maxime U. Garcia
91b5875b44
Merge pull request #331 from nf-core/praveenraj2018-patch-1 
Added: runOptions to singularity
 2022-02-14 13:12:11 +01:00
Maxime U. Garcia
41e00ae8f9
Update conf/munin.config 2022-02-14 13:11:46 +01:00
Praveen Raj S
90936a5518
Added: runOptions to singularity 
To bind external mount directories at runtime.
 2022-02-14 12:45:20 +01:00
Combiz Khozoie
2d434c6ee5
Merge pull request #321 from nf-core/combiz-patch-1 
Imperial config updates
 2022-02-11 14:49:30 +00:00
Maxime U. Garcia
4a936a685e
Merge pull request #317 from nf-core/praveenraj2018-patch-1 
Added genome parameter
 2022-02-11 15:33:18 +01:00
Combiz Khozoie
a77f718ae2
Merge pull request #330 from nf-core/master 
Pulling master to branch
 2022-02-11 14:18:01 +00:00
Matthias Hörtenhuber
0d18767d0c
Merge pull request #329 from mashehu/master 
update node version for markdownlint
 2022-02-11 14:32:38 +01:00
Matthias Hörtenhuber
b98ab26662 fix markdownlint errors 2022-02-11 14:09:16 +01:00
Matthias Hörtenhuber
fcc856c8da update node version for markdownlint 2022-02-11 11:03:18 +00:00
Combiz Khozoie
3ce32f50c4
Update imperial.config 
Moved params configs from internal profile to universal
 2022-02-11 11:02:40 +00:00
Combiz Khozoie
683564de1b
Update main.yml 
Removed deprecated imperial medbio from GHA
 2022-02-11 09:35:18 +00:00
Combiz Khozoie
8937699abe
Update README.md 
Added imperial docs link
 2022-02-11 09:33:54 +00:00
Combiz Khozoie
f33bc965d6
Update nfcore_custom.config 
Removed deprecated medbio config
 2022-02-11 09:32:50 +00:00
Combiz Khozoie
b99b74b2d3
Update imperial.config 
Fixed indent
 2022-02-11 00:26:45 +00:00
Combiz Khozoie
c5e4ac2025
Update scflow.config 
Removed line corresponding to profile deprecated by change to internal profiles
 2022-02-11 00:25:44 +00:00
Combiz Khozoie
34d9e7a967
Update imperial.md 
Updated docs to reflect use of internal profiles
 2022-02-11 00:08:08 +00:00
Combiz Khozoie
5aa1abda26
Delete imperial_mb.md 
Deprecated in favour of internal profiles within the single imperial.config
 2022-02-11 00:07:05 +00:00
Combiz Khozoie
14c7662762
Update imperial.md 
Updated docs to reflect restructuring for internal profiles
 2022-02-10 23:49:43 +00:00
Combiz Khozoie
38a05a6531
Update imperial.config 
Reworked to use internal profiles for the Imperial HPC and the MedBio cluster.
 2022-02-10 23:46:14 +00:00
Combiz Khozoie
e1d0bf0cd2
Delete imperial_mb.config 
Separate config for the medbio queue now deprecated in favour of an internal profile within the main imperial.config
 2022-02-10 23:44:49 +00:00
Combiz Khozoie
fe5474a029
Update imperial.config 
Multiple process level updates reflecting the latest job sizing guidelines for the Imperial HPC
 2022-02-10 23:02:47 +00:00
Harshil Patel
8fa6ab9b35
Merge pull request #323 from stevin-wilson/patch-1 
Added ARTIC v4.1 primer set information
 2022-02-10 19:17:47 +00:00
James A. Fellows Yates
92424ee2c3
Merge pull request #328 from jfy133/eva-update 
eager @ EVA walltime whole year
 2022-02-10 17:23:04 +01:00
James Fellows Yates
88ddc9eee7 fffff 2022-02-10 11:34:57 +01:00
James Fellows Yates
d7d0f5cecc Change base time 2022-02-10 11:32:49 +01:00
James Fellows Yates
dbd78f8075 Re add . 2022-02-10 11:26:18 +01:00
James Fellows Yates
dd94895f16 remove quotes 2022-02-10 11:22:45 +01:00
James Fellows Yates
39c2d9b25b Oops 2022-02-10 11:19:16 +01:00
James Fellows Yates
c0ee3225ad Add times for 365d 2022-02-10 11:02:52 +01:00
James A. Fellows Yates
192839c8be
Merge pull request #327 from nf-core/TCLamnidis-patch-2 
Removed all time limits
 2022-02-10 10:22:53 +01:00
Thiseas C. Lamnidis
fa4075c2a0
Removed all time limits 2022-02-10 10:00:18 +01:00
James A. Fellows Yates
64355b84d2
Merge pull request #325 from jfy133/eva-update 
Read add empty BAM exit code for qualimap 255 for eager @ EVA
 2022-02-08 11:28:36 +01:00
James A. Fellows Yates
2b06293f64
Read add empty BAM exit code for qualitmap 255 2022-02-08 11:15:17 +01:00
James A. Fellows Yates
8d286e3b69
Merge pull request #324 from jfy133/eva-update 
New attempt of workaround SGE + Java incompatibility for eager @ EVA
 2022-02-06 20:02:03 +01:00
James A. Fellows Yates
8c5a54ac9f
Update conf/pipeline/eager/eva.config 2022-02-06 19:37:53 +01:00
James A. Fellows Yates
aa525c6ebf
Allow exit code 1 retry for all java processes 2022-02-06 09:07:53 +01:00