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410 commits

Author SHA1 Message Date
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
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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
drpatelh
bcb8950c2f Change URL to website 2019-12-18 10:57:12 +00:00
drpatelh
be5ed21269 Update docs 2019-12-18 10:54:31 +00:00
drpatelh
0779d25255 Update docs 2019-12-12 13:02:51 +00:00
Alexander Peltzer
a6d08ed646
Adjust custom pipeline config for ampliseq on BINAC 2019-12-11 16:09:44 +01:00
Maxime Garcia
9497b78149
Merge pull request #100 from MaxUlysse/UPPMAX 
Improve UPPMAX configs
 2019-12-06 10:52:44 +01:00
Maxime Garcia
79528de92f
Update docs/uppmax.md 
Co-Authored-By: Phil Ewels <phil.ewels@scilifelab.se>
 2019-12-06 10:47:09 +01:00
jfy133
1650080b6e Linting 2019-12-05 17:03:07 +01:00
jfy133
731372dac2 Added SHH specific EAGER configuration 2019-12-05 17:01:10 +01:00
MaxUlysse
a63ec24626 Merge branch 'UPPMAX' of github.com:MaxUlysse/nf-core_configs into UPPMAX 2019-12-05 15:18:04 +01:00
MaxUlysse
99afe86ea9 update docs 2019-12-05 15:18:01 +01:00
Maxime Garcia
78826c9d4e
Merge branch 'master' into UPPMAX 2019-12-05 12:52:34 +01:00
Alexander Peltzer
9cdb915efb
Merge pull request #101 from jfy133/master 
Condensing SHH profile(s) with sub-profiles
 2019-12-05 12:51:31 +01:00
jfy133
54dafbcfa3 Condensing SHH profiles following https://github.com/nf-core/configs/pull/100 2019-12-05 12:09:11 +01:00
MaxUlysse
cdbdbee0eb replace -profile uppmax_devel by -profile uppmax,devel 2019-12-05 11:49:44 +01:00
Maxime Garcia
2669401a72
Merge branch 'master' into sarek 2019-11-27 13:27:43 +01:00
James A. Fellows Yates
c725c71e4d
Merge branch 'master' into master 2019-11-26 20:34:42 +01:00
jfy133
6f40c13473 Split shh config for each cluster 2019-11-26 20:20:17 +01:00
phue
672f025639 cbe: add documentation about iGenomes 2019-11-26 18:09:20 +01:00
Alexander Peltzer
81739a3907
Merge pull request #93 from jfy133/master 
Updated max resources for SHH SDAG
 2019-11-26 15:56:39 +01:00
James A. Fellows Yates
89506a653c
Remove empty lines in block quotes for linting 2019-11-26 15:34:25 +01:00
James A. Fellows Yates
12ec22838c
Specified max sources currently at SDAG limits (exceeds cdag) 2019-11-26 15:29:03 +01:00
noirot
07b1f17d6a correct md to pass linter 2019-11-26 15:02:06 +01:00
Noirot Céline
3ed206b7a7
Update docs/genotoul.md 
ok

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
 2019-11-26 14:52:45 +01:00
Noirot Céline
288294994e
Update docs/genotoul.md 
ok

Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
 2019-11-26 14:52:32 +01:00
noirot
e95196451f correct md to pass linter 2019-11-26 14:47:23 +01:00
noirot
42c949db95 correct md to pass linter 2019-11-26 14:43:42 +01:00
Alexander Peltzer
23f9fd2d73
Merge branch 'master' into master 2019-11-26 14:20:36 +01:00
Noirot Céline
42d99e7006
Update genotoul.md 2019-11-26 13:18:34 +01:00
Maxime Garcia
f6c2e4c65f Update docs/pipeline/sarek/munin.md 
Update conf/pipeline/sarek/munin.config

testing out module and containers collision
 2019-11-26 11:57:51 +01:00
MaxUlysse
25d4e92935 update docs 2019-11-26 11:55:36 +01:00
Maxime Garcia
b029ccaa59 Update docs/pipeline/sarek/munin.md 
Update conf/pipeline/sarek/munin.config
 2019-11-26 11:48:11 +01:00
MaxUlysse
283abcece4 update docs 2019-11-26 11:25:29 +01:00
MaxUlysse
cd1d0b5f8f Add specific sarek config base, munin specific sarek config and docs 
rename file

improve configs

remove unnecessary params
 2019-11-26 11:25:29 +01:00
Alexander Peltzer
aeb2fb6dc0
Fix all the markdownlinting errors 2019-11-26 00:48:17 +01:00
Noirot Céline
ed4436c1a6
Merge branch 'master' into master 2019-11-25 16:24:12 +01:00
noirot
db51c49b2f Add genotoul config 2019-11-25 14:54:25 +01:00
MaxUlysse
08a6b74825 add new profile to be shared: awsbatch 2019-11-19 14:16:06 +01:00
Alexander Peltzer
d2603a134e
Add in denbi cloud configs 2019-11-11 12:26:19 +01:00
Phil Ewels
6790dbd4a3
Merge pull request #82 from arontommi/dev 
documentation on how to fix bianca "Requested node configuration is not available" problem
 2019-11-08 15:07:07 +01:00
Phil Ewels
5e7d13df89
Update uppmax.md 2019-11-08 10:59:34 +01:00
arontommi
3f534c154e documentation on how to fix bianca cluster configuration problem 2019-11-07 13:06:31 +01:00
arontommi
99f4d9b9bd documentation on how to fix bianca cluster configuration problem 2019-11-06 13:10:09 +01:00
maxibor
47a7d57db4 update shh doc 2019-10-28 16:09:00 +01:00
phue
5a9dbe5d7c MENDEL is no more 
the cluster is no longer operational, was replaced by CBE
 2019-10-28 14:11:34 +01:00
Alexander Peltzer
5348b8c609
Revert "BINAC SMP / Short / Long Updates" 2019-10-28 13:12:31 +01:00
Alexander Peltzer
b5b2dd817f
Merge all 2019-10-27 13:24:45 +01:00