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195 commits

Author SHA1 Message Date
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
Anthony Bretaudeau
883a761651 add link 2019-10-16 18:45:26 +02:00
Anthony Bretaudeau
1f2786c78f add genouest cluster 2019-10-16 18:15:04 +02:00
phue
9b3fda36f6 update singularity version
singularity/3.1.0 is not available anymore
2019-10-10 21:22:19 +02:00
phue
5e257e7e9a add cbe profile 2019-09-22 16:45:09 +02:00
MaxUlysse
f69524d59a feat: update docs 2019-08-07 11:56:10 +02:00
MaxUlysse
332ba0dadb fix: update and rearrange munin configuration file and docs 2019-08-07 11:10:48 +02:00
Martin Proks
c583aa0233 Added kraken config (#15)
* Added kraken template
* docs: updated some info
* fix: updated igenomes_base path
2019-08-05 11:19:05 +02:00
Alexander Peltzer
82ffedf895
Drop aquila 2019-07-30 18:53:36 +02:00
Alexander Peltzer
4e48d4cc62
Fix remaining points by drpatelh 2019-07-30 18:53:00 +02:00
Alexander Peltzer
35c715ca3b
Merge remote-tracking branch 'upstream/master' 2019-07-30 16:53:19 +02:00
Remi Planel
1c0d596582 Merge remote-tracking branch 'upstream/master' 2019-07-30 16:15:20 +02:00
Remi Planel
be28a34839 Updat Pasteur doc 2019-07-30 16:12:30 +02:00
Remi Planel
64e78a3dc1 Update the doc 2019-07-30 15:17:25 +02:00
Remi Planel
6f264ac2ca Add pasteur profile doc 2019-07-30 15:15:30 +02:00
marchoeppner
b74f020f14
Update docs/ccga_dx.md
Co-Authored-By: Harshil Patel <drpatelh@users.noreply.github.com>
2019-07-29 12:45:30 +02:00