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416 commits

Author SHA1 Message Date
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
b98ab26662 fix markdownlint errors 2022-02-11 14:09:16 +01:00
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
phue
a6dd3aa0f1 cbe: update recommended nextflow version in docs
otherwise, the new anaconda requirements will cause conflicts
2022-02-04 10:21:52 +01:00
Lara Ianov
f876227a38 added note on screen, conda, and interactive partitions 2022-01-28 12:18:11 -06:00
Austyn Trull
06541411dd Initial commit of cheaha profile 2022-01-28 11:37:42 -06:00
Kevin Brick
afb6fbb767
Trailing spaces 2021-12-17 00:46:50 -05:00
Kevin Brick
05f7b59573
Update nihbiowulf.md 2021-12-17 00:44:39 -05:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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