Kevin Brick
9cf4f69ff3
Add files via upload
2021-12-17 00:37:11 -05:00
praveenraj2018
00a3ed0fa6
Formatting
2021-12-14 21:24:18 +01:00
Praveen
b4d5330c0e
Added rnavar pipeline config for Munin
2021-12-14 03:52:37 +01:00
PCQ
a72f1a243c
Create marvin.md
2021-12-10 17:39:32 +01:00
Venkat Malladi
d722e7206e
Fix readme to remove blob account.
2021-11-18 18:06:54 -06:00
Phil Ewels
4785ceccba
Merge pull request #245 from ikeller/unibe_ibu
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Unibe ibu
2021-11-19 00:56:25 +01:00
Phil Ewels
b25bd1ce42
Update docs/azurebatch.md
2021-11-19 00:54:39 +01:00
Venkat Malladi
ed4c1d5f22
Remove work_dir option.
2021-11-18 17:52:24 -06:00
Phil Ewels
286fa6753a
Apply suggestions from code review
2021-11-19 00:07:33 +01:00
Phil Ewels
a26b3bf1e3
Merge branch 'master' into unibe_ibu
2021-11-19 00:02:30 +01:00
Venkat Malladi
f25dc57f00
Fix headers.
2021-11-18 15:50:12 -06:00
Venkat Malladi
1dacc2f3fe
Fix liniting errors in headers.
2021-11-18 15:49:08 -06:00
Venkat Malladi
845a9ce971
Update Readme with more inforamtion on the options.
2021-11-18 15:47:27 -06:00
Venkat Malladi
219244f1b4
Add in sample datastorage for Illumina Platinum genomes.
2021-11-18 15:28:34 -06:00
Venkat Malladi
237f91a3b7
Add in minmum config for azure.
2021-11-18 14:51:39 -06:00
Harshil Patel
a098ad9e06
Add Chris as main contact at The Crick
2021-11-03 11:11:05 +00:00
Matiss Ozols
5222d7ed9b
added leicester profile
2021-10-21 19:08:06 +01:00
Matiss Ozols
1f58ea42c7
added leicester profile
2021-10-21 19:06:03 +01:00
Matiss Ozols
98a69683c2
added leicester profile
2021-10-21 19:04:48 +01:00
Matiss Ozols
f8b932ae2d
added leicester profile
2021-10-21 18:32:57 +01:00
James A. Fellows Yates
73b6b74c69
Merge pull request #279 from pierrespc/master
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Added Configuration files for running in Maestro HPC at Pasteur Institute, Paris
2021-10-08 19:15:47 +02:00
James A. Fellows Yates
98bbc2b744
Linting
2021-10-08 14:11:39 +02:00
James A. Fellows Yates
b26e495e19
Apply suggestions from code review
2021-10-08 14:08:51 +02:00
pierrespc
2d102eafbc
format docs
2021-10-08 13:46:47 +02:00
pierrespc
035ab61f61
added unlimitedtime profile to maestro; changed cache for bwa process
2021-10-08 09:05:46 +02:00
pierrespc
1621585558
improving documentation
2021-10-04 16:08:33 +02:00
pierrespc
e5d4a357c5
clean doc
2021-10-04 15:08:01 +02:00
pierrespc
136fd44e0c
corrected docs/maestro.config
2021-09-29 13:50:56 +02:00
James A. Fellows Yates
e8b48416bc
Update docs/alice.md
2021-09-28 12:52:31 +02:00
Bjørn Peare Bartholdy
ad83430632
Update docs/alice.md
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-28 12:43:54 +02:00
Bjørn Peare Bartholdy
197bd6cfb1
Merge branch 'nf-core:master' into master
2021-09-28 12:09:50 +02:00
bbartholdy
b6ccb46383
add ALICE profile
2021-09-28 12:08:27 +02:00
Mei Wu
c2d74b290a
fix md
2021-09-27 16:25:02 +02:00
Mei Wu
a8a2027f70
Merge branch 'master' into hasta
2021-09-27 16:12:23 +02:00
Mei Wu
ae0adb056f
initial commit
2021-09-27 16:05:19 +02:00
pierrespc
3b593d46ec
merged two pasteur config files for maestro
2021-09-20 15:14:50 +02:00
Harshil Patel
5068e4806f
Merge pull request #271 from theoportlock/master
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Adds Rosalind config for KCL!
2021-09-17 13:36:19 +01:00
theoportlock
0fd5265f7b
Updates the README
2021-09-17 13:21:38 +02:00
pierrespc
b9682bbc91
requires files edited
2021-09-16 12:53:17 +02:00
Marc Trunjer Kusk Nielsen
9a8644ef43
Update computerome.md
2021-09-15 11:10:02 +02:00
Marc Trunjer Kusk Nielsen
cf899a2a4e
Update computerome.md
2021-09-13 08:48:27 +02:00
Marc Trunjer Kusk Nielsen
f46172c25b
Update computerome.md
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Update with usage, heavily inspired by the UPPMAX docs
2021-09-13 08:16:11 +02:00
Marc Trunjer Kusk Nielsen
463df26c72
Merge branch 'nf-core:master' into computerome
2021-09-10 14:47:05 +02:00
theoportlock
b240142cc3
Adds rosalind configuration
2021-09-08 14:33:39 +02:00
Rogan Grant
54298ca0f7
Merge branch 'nf-core:master' into master
2021-09-04 15:37:03 -05:00
Marc Trunjer Kusk Nielsen
aad2486215
Create computerome.md
2021-08-31 14:10:19 +02:00
James Fellows Yates
59af7f0eee
Delete SHH profiles due to decommissioning
2021-08-20 10:15:39 +02:00
Rogan Grant
f793ffaace
Updated iGenomes location
2021-08-03 15:10:54 -05:00
Rogan Grant
079258ebbb
Minor text edits
2021-07-29 11:38:40 -05:00
Rogan Grant
482478878d
Added instructions for module loading
2021-07-28 18:11:10 -05:00
Rogan Grant
40170632aa
First draft of markdown file, with instructions for installing nextflow and getting access
2021-07-28 13:04:32 -05:00
Barry digby
ef6b13e377
tabs rm
2021-07-28 12:19:11 +01:00
Barry digby
f62298d211
w
2021-07-28 11:44:06 +01:00
Barry digby
2fc8082aad
w
2021-07-28 11:43:39 +01:00
Barry digby
11cb6cc70d
w
2021-07-28 11:41:42 +01:00
Barry digby
380adf083a
markdowwwwn
2021-07-28 11:41:16 +01:00
Barry digby
2a06d956b3
mdlint so picky : (
2021-07-27 17:18:42 +01:00
Barry digby
2b6e80561a
Merge branch 'master' of https://github.com/nf-core/configs into
2021-07-27 17:13:17 +01:00
Barry digby
04c0da5a2f
nuig confg (lugh)
2021-07-27 17:05:27 +01:00
ameynert
5224eb5574
Updated resources folder & institute name
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Local resources folder was re-organized & re-named BioinformaticsResources. Added note about viralrecon & atacseq pipeline-specific config. IGMM name-changed recently; updated to IGC.
2021-07-21 12:15:17 +01:00
Maxime U. Garcia
30e058abf0
Merge branch 'master' into master_kraken
2021-07-20 09:26:56 +02:00
Gisela Gabernet
e2088a008d
Merge branch 'master' into master
2021-07-03 12:24:42 +02:00
ggabernet
ee2e8392ab
add aws_tower profile
2021-07-03 12:17:21 +02:00
Edmund Miller
21e1037e0c
docs(sysbio): Add rnaseq specific docs
2021-06-17 09:18:45 -05:00
Edmund Miller
41ae99d34a
feat(sysbio): Add cleanup
2021-06-17 08:17:55 -05:00
Edmund Miller
87c8e346e0
fix(sysbio): Change filetype
2021-06-17 08:14:48 -05:00
Edmund Miller
2a958f5ce3
docs: Add sysbio
2021-06-16 21:19:38 -05:00
ikeller
af1e57027d
edit config and readme
2021-05-19 09:46:07 +02:00
Barry digby
24a4119e43
memory test
2021-04-29 14:24:57 +01:00
Barry digby
8340e89768
nuig.config first commit
2021-04-28 17:28:01 +01:00
Alexander Peltzer
c12c373969
Merge pull request #235 from aunderwo/cambridge
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Add Cambridge University HPC config
2021-04-25 10:40:56 +02:00
Anthony Underwood
982d1a8f2a
Fix markdown linting
2021-04-22 16:41:05 +01:00
Anthony Underwood
29dcc160e3
Create cambridge.md
2021-04-22 16:04:29 +01:00
Anthony Underwood
3e8f9b3d4e
Remove blank lines
2021-04-22 15:57:09 +01:00
Anthony Underwood
f414446a88
Add info on how to load Singularity into your path
2021-04-22 15:38:36 +01:00
Anthony Underwood
b16b011bcc
Add ~/bin as recommended location for nextflow executable
2021-04-22 12:02:11 +01:00
Anthony Underwood
cc18d213dc
Update sanger.md
2021-04-21 20:24:08 +01:00
Anthony Underwood
40eb3e0201
Update sanger.md
2021-04-21 20:20:30 +01:00
Anthony Underwood
7163e8723d
Create sanger.md
2021-04-21 20:17:42 +01:00
Maxime Garcia
1548690ca6
Update docs/uppmax.md
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Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
2021-04-21 12:27:27 +02:00
MaxUlysse
bab9241243
fix: markdownlint
2021-04-21 11:51:14 +02:00
MaxUlysse
844246cc7d
fix: clearer usage of module
2021-04-21 11:28:58 +02:00
MaxUlysse
1a7ec56c33
feat: more details
2021-04-21 11:23:50 +02:00
MaxUlysse
c89877decc
feat: use <PIPLEINE>
2021-04-21 11:17:06 +02:00
MaxUlysse
658fa7ccda
fix: markdownlint
2021-04-21 11:08:16 +02:00
Maxime Garcia
79e3dd65a7
Apply suggestions from code review
...
Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
2021-04-21 11:06:39 +02:00
Maxime Garcia
4eea06f0db
Apply suggestions from code review
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Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
2021-04-20 16:03:34 +02:00
MaxUlysse
1c1dd952fc
fix: bullet list
2021-04-20 15:58:51 +02:00
Maxime Garcia
e4d2ef0984
Apply suggestions from code review
...
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
2021-04-20 15:53:54 +02:00
MaxUlysse
4930795cab
feat: more complete docs
2021-04-20 15:38:49 +02:00
MaxUlysse
10abca712b
fix: first draft of bianca guide
2021-04-16 17:01:58 +02:00
James A. Fellows Yates
12a4518803
Markdown lint fix
2021-04-15 22:29:15 +02:00
James A. Fellows Yates
0fc90586e0
Update mpcdf.md
2021-04-15 22:26:37 +02:00
MaxUlysse
3918e0aa9d
feat: remove kraken profile
2021-04-13 15:14:14 +02:00
James A. Fellows Yates
161c3a33d4
Merge branch 'master' into eva
2021-04-07 19:28:16 +02:00
Alexander Peltzer
91f50aad4e
Merge pull request #221 from phue/biohpc_gen
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Add BioHPC Genomics config
2021-04-07 14:03:22 +02:00
James Fellows Yates
8dac4ca552
Merge branch 'eva' of github.com:jfy133/configs into eva
2021-04-06 17:53:32 +02:00
James Fellows Yates
60c66d93ac
Markdown linting
2021-04-06 17:53:27 +02:00
James A. Fellows Yates
832edaa450
Merge branch 'master' into eva
2021-04-06 17:51:46 +02:00
James Fellows Yates
be1d35840d
Add EVA and EAGER@EVA
2021-04-06 17:48:16 +02:00
ameynert
700776f759
Change to shared Singularity cache
2021-03-30 16:11:15 +01:00
phue
7c5a0871a3
add note about required nextflow version
2021-03-29 19:36:49 +02:00
phue
8fc60e2e70
add config for biohpc_gen
2021-03-29 19:25:58 +02:00
Gisela Gabernet
71a97ba316
Merge pull request #185 from ggabernet/master
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awsbatch config update
2021-03-28 20:59:40 +02:00
ameynert
3a8e54f153
Removed sneaky trailing whitespace.
2021-03-24 13:58:10 +00:00
ameynert
a0d42f5153
Fixed code blocks for markdown linting
2021-03-24 13:55:31 +00:00
Phil Ewels
bfab371c94
Merge branch 'master' into master
2021-03-24 12:36:15 +01:00
ameynert
2a8ae2b214
Update eddie.md
2021-03-24 11:12:41 +00:00
ameynert
96fe6185a0
IGMM-specific docs
2021-03-24 11:01:41 +00:00
Asaf Peer
9b2d5bfead
Merge pull request #216 from asafpr/master
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Added JAX conf
2021-03-24 03:31:14 -04:00
ameynert
791f3c95f3
Pipeline specific configs moving to confs/pipeline
2021-03-23 16:07:07 +00:00
Alexander Peltzer
5988c51361
Merge pull request #211 from DoaneAS/master
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Adding WCM.config for Weill Cornell Medicine cluster
2021-03-23 14:58:27 +01:00
Asaf Peer
30c864e112
added JAX conf
2021-03-21 06:49:11 -04:00
ameynert
b48136a62e
Added pipeline-specific config files
2021-03-18 12:55:03 +00:00
ameynert
af6a6b1060
Details on running on eddie
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Removed Conda support, Singularity by default. Added login and screen session on wild west node options.
2021-03-18 12:48:48 +00:00
ameynert
4ad6bb2bec
Singularity info
2021-03-17 14:50:40 +00:00
Noirot Céline
e3216ccf79
typo
2021-03-16 16:00:56 +01:00
Noirot Céline
cc17045914
Add institution
2021-03-16 15:58:29 +01:00
Noirot Céline
7e9f83ee81
Add IFB config
2021-03-16 15:54:19 +01:00
Ashley S Doane
6343a7f87c
Update wcm.md
2021-03-11 14:01:07 -05:00
Ashley S Doane
d630bcfb6c
Create wcm.md
2021-03-11 13:59:55 -05:00
ameynert
4c0111f598
Eddie profile documentation initial commit
2021-03-04 14:46:58 +00:00
James A. Fellows Yates
0bac3691e3
Create mpcdf.config
2021-02-14 18:07:40 +01:00
James Fellows Yates
a78aac327d
Linting fixes
2021-02-14 17:58:50 +01:00
James Fellows Yates
537f52a640
Add MPI-EVA profile
2021-02-14 17:50:20 +01:00
ggabernet
0909708b97
update with upstream
2021-02-09 22:01:27 +01:00
Charles Plessy
1608b36dcf
Institutional profile for Okinawa Institute of Science and Technology
2021-02-02 17:40:10 +09:00
James A. Fellows Yates
c4604450d8
Update seg_globe.md
2021-01-21 13:04:12 +01:00
Åshild J. Vågene
bcd137225e
Update and rename ceh.md to seg_globe.md
2021-01-21 11:46:46 +01:00
Åshild J. Vågene
ef80452577
Update docs/ceh.md
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-01-21 11:16:46 +01:00
James A. Fellows Yates
2fd475c339
Fix some linting errors
2021-01-21 06:30:43 +01:00
Åshild J. Vågene
d108666950
Update ceh.md
2021-01-21 00:30:54 +01:00
Åshild J. Vågene
65831b73ef
Create ceh.md
2021-01-21 00:17:08 +01:00
Combiz Khozoie
a61992d144
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
arontommi
ac108379cd
trailing spaces
2020-11-26 13:58:16 +01:00
arontommi
c2c7265518
fix linting errors
2020-11-26 13:47:47 +01:00
arontommi
6480aef1db
typo
2020-11-26 11:41:33 +01:00
arontommi
f84fbb8f89
typo
2020-11-26 11:39:51 +01:00
arontommi
e6bb7a4852
capital names
2020-11-26 11:37:59 +01:00
arontommi
5726ef3456
typo
2020-11-26 11:26:08 +01:00
arontommi
06469901fe
typo
2020-11-26 11:24:29 +01:00
arontommi
ebf754bf43
documentation for bianca
2020-11-26 09:53:51 +01:00
Phil Ewels
e96455e180
Update docs/uppmax.md
2020-11-26 01:43:09 +01:00
Phil Ewels
d9a8009662
Better UPPMAX docs
2020-11-25 22:45:16 +01:00
Andrew Frank
d70fc2605a
Fix parameters in google.md
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Change parameters from hyphens to underscores to accurately reflect google.config
2020-11-12 11:52:58 -05:00
Gisela Gabernet Garriga
885f0ce5f6
awsbatch config update
2020-11-09 22:41:38 +01:00
lecorguille
e3d733d87e
Add ABiMS - fix lint
2020-10-23 09:29:54 +02:00
lecorguille
4d03f72c78
Add ABiMS - last bits of doc
2020-10-23 09:27:12 +02:00
lecorguille
6ee6b7bf56
Add ABiMS - remove a useless link
2020-10-23 00:12:02 +02:00
lecorguille
23ba1c58b1
Add ABiMS - NXF_SINGULARITY_CACHEDIR
2020-10-23 00:11:58 +02:00
lecorguille
f21d16b24f
Add ABiMS - fix lint
2020-10-22 17:47:25 +02:00
lecorguille
a63ca751ee
Add ABiMS
2020-10-22 16:57:41 +02:00
James A. Fellows Yates
7088ed196f
Update mpcdf.md
2020-10-22 11:08:29 +02:00
James A. Fellows Yates
0d6e269322
Update mpcdf.md
2020-10-15 14:24:08 +02:00
James A. Fellows Yates
9df85be081
Update mpcdf.md
2020-09-03 20:27:15 +02:00
James A. Fellows Yates
09cd5cad65
Update mpcdf.md
2020-09-03 20:25:37 +02:00
James A. Fellows Yates
0501ae4c1a
Started docs for mpcdf
2020-09-03 20:21:49 +02:00
James A. Fellows Yates
09cfabd37f
Add new microbiome_screening profile to docs
2020-08-11 09:20:31 +02:00
drpatelh
165af5122f
Update docs
2020-08-03 11:39:23 +01:00
jfy133
15dad7e2e7
Add caveats for EAGER @ SHH profiles
2020-07-08 09:47:03 +02:00
James A. Fellows Yates
b2e043ab59
Add documentation for HOPS profile for eager @ SHH
2020-07-07 14:35:42 +02:00
Phil Ewels
cd9fbb22dc
Merge pull request #161 from ewels/uct_hpc
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Update UCT hex -> hpc
2020-06-22 09:18:43 +02:00
Phil Ewels
29f5fa6ce4
uct_hpc docs, readme
2020-06-17 15:22:42 +02:00
Phil Ewels
17824d2d62
Merge czbiohub_aws_highpriority profile into czbiohub_aws
2020-06-16 15:20:39 +02:00
phue
6d356cc918
CBE: don't load singularity module
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singularity is now installed from CentOS repos, the environment module will be removed
2020-06-05 12:07:26 +02:00
Alexander Peltzer
f877644059
Merge branch 'master' into master
2020-05-29 11:43:47 +02:00
Alexander Peltzer
dd56355c7c
Update bi.md
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No trailing spaces it said.
2020-05-28 10:18:16 +02:00
Alexander Peltzer
f4df5b5a75
Add BI Docs
2020-05-28 10:16:22 +02:00
Alexander Peltzer
6011419454
Merge pull request #154 from jfy133/master
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Update SHH nf-core/eager group-specific profiles
2020-05-27 17:52:09 +02:00
James A. Fellows Yates
0943ba088a
Mention SHH EAGER group-specific profiles
2020-05-26 11:14:42 +02:00
James A. Fellows Yates
2e3b577fb3
Typo fixes
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I'll never forgive our directory for that name...
2020-05-07 11:50:11 +02:00
James A. Fellows Yates
38e9e54932
Merge pull request #151 from jfy133/master
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Add additional custom nf-core/eager params for SHH profile
2020-05-07 09:25:02 +02:00
James A. Fellows Yates
0a312cd2c9
Update shh.md
2020-05-07 09:17:56 +02:00
James A. Fellows Yates
4804052b23
Update SHH nf-core/eager pipeline docs
2020-05-04 21:04:17 +02:00
MaxUlysse
e6f4d58fa6
update rnafusion munin specific config
2020-04-28 17:06:04 +02:00
Adrian
1e68a10ef0
adding documentation for icr_davros
2020-04-28 16:02:26 +01:00
MaxUlysse
50a44d037b
better docs and organisation of giles
2020-04-09 17:02:36 +02:00
Daniel Lundin
c8de9be701
Adding UPPMAX specific config for ampliseq
2020-03-31 15:17:24 +02:00
MaxUlysse
d4bea56f52
add munin/rnafusion specific docs + markdownlint
2020-03-11 14:23:23 +01:00
MaxUlysse
7c60096952
update docs for munin/sarek specific config
2020-03-11 14:17:24 +01:00
MaxUlysse
250035e71d
fix path to config files
2020-03-11 14:11:23 +01:00
Edmund Miller
1c62395332
docs(utd_ganymede): add initial documentation
2020-03-09 20:07:46 -05:00
James A. Fellows Yates
52214cc22d
Merge pull request #134 from marcel-keller/ebc
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adding Estonian Biocentre cluster profile
2020-03-09 16:09:27 +01:00
marcel-keller
dcb478c904
Update ebc.md
2020-03-09 17:07:03 +02:00
marcel-keller
88cfe11187
Update ebc.md
2020-03-09 16:32:14 +02:00
marcel-keller
418f4b52b6
Create ebc.md
2020-03-09 16:23:16 +02:00
Alexander Peltzer
b8d020b78c
Update cfc.md
2020-03-09 15:12:49 +01:00
Evan Floden
6141e008a3
Update google.md
2020-03-09 14:44:58 +01:00
Evan Floden
d8ad376f71
Merge branch 'master' into master
2020-03-06 10:29:50 +00:00
Evan Floden
f5364e45e7
Update google.md or markdown linting
2020-03-06 11:27:44 +01:00
Alexander Peltzer
59a787b179
Merge pull request #122 from marchoeppner/ccga-config
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Removing old CCGA profile from docs and linting
2020-03-06 11:17:08 +01:00
mseybold
2135996b13
Update cfc.md
2020-03-06 11:12:21 +01:00
Evan Floden
87e8da61a4
Readme formatting
2020-03-06 05:58:59 +00:00
Evan Floden
8a9d3ad8a0
First commit of Google Cloud config
2020-03-06 05:47:29 +00:00
Marc Hoeppner
6c5a5c8bcb
Removing old CCGA profile from docs and linting
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Removing CCGA profile from master config
Removing CCGA profile from master config
2020-02-24 12:16:33 +01:00
Maxime Garcia
08e2804b37
Merge branch 'master' into Uppmax
2020-02-20 17:18:46 +01:00
MaxUlysse
aa905cd645
add UPPMAX specific sarek config
2020-02-20 17:14:18 +01:00
marchoeppner
0830203b70
Adding new CCGA Med Cluster to profiles
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Updating README and fixing linting errors in CCGA_MED profile
Fixing order in profile queue and removed leading slash from readme for ccga profile docs
Fixing order in profile queue and removed leading slash from readme for ccga profile docs
2020-02-11 11:12:51 +01:00
James A. Fellows Yates
799f2d5788
Grammar tweak
2019-12-21 20:59:48 +01:00
James A. Fellows Yates
435a5892ea
Updated docs corresponding to 638758423a
2019-12-21 20:59:25 +01:00