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687 commits

Author SHA1 Message Date
drpatelh
165af5122f Update docs 2020-08-03 11:39:23 +01:00
drpatelh
b804076959 Remove hard Singularity version 2020-08-03 11:38:10 +01:00
Alexander Peltzer
11f6107922
Merge pull request #174 from maxibor/master
Add temporary CDAG setting for SHH config
2020-07-23 16:09:28 +02:00
maxibor
69a0bd572b add temporary CDAG setting for SHH config 2020-07-23 15:38:28 +02:00
James A. Fellows Yates
d38ffc289b
Merge pull request #173 from jfy133/shh-eager-hops-update
Remove now deprecated EAGER flag for HOPS profile
2020-07-20 11:34:49 +02:00
James A. Fellows Yates
57ac9257a9
Remove now deprecated EAGER flag for HOPS profile 2020-07-20 11:29:12 +02:00
Alexander Peltzer
a498e98342
Merge pull request #170 from jfy133/master
Make walltimes more sophisticated and add a HOPS profile for nf-core/eager @ SHH
2020-07-15 15:11:24 +02:00
James A. Fellows Yates
84e03b8264
Re-bump default walltimes after debugging/testing 2020-07-11 18:31:04 +02:00
James A. Fellows Yates
8f6409d144
Remove min support percent value to avoid confusion 2020-07-08 15:26:19 +02:00
James A. Fellows Yates
1af9ce293c
Update hops profile based on requests from pathogen group 2020-07-08 15:22:33 +02:00
James A. Fellows Yates
c57a404f18
Add desc for hops 2020-07-08 10:45:43 +02:00
jfy133
15dad7e2e7 Add caveats for EAGER @ SHH profiles 2020-07-08 09:47:03 +02:00
jfy133
926c14f7ee Cleverer process time submission 2020-07-08 09:36:56 +02:00
jfy133
563c27e1bb Try again to get better time resource submission 2020-07-08 09:36:28 +02:00
James A. Fellows Yates
c6905b609e
Update shh.config 2020-07-08 09:25:21 +02:00
James A. Fellows Yates
b360ce26bc
Update shh.config 2020-07-08 09:24:06 +02:00
James A. Fellows Yates
31edb4b5d7
Update shh.config 2020-07-08 09:20:00 +02:00
James A. Fellows Yates
aac3478e86
Add better task time values to account for large data 2020-07-08 09:12:11 +02:00
James A. Fellows Yates
737d826932
Update shh.config 2020-07-08 08:36:04 +02:00
piotr-faba-ardigen
ba24f1a1c8
Merge pull request #168 from piotr-faba-ardigen/add_bi_config
Fix bi config
2020-07-07 14:56:43 +02:00
James A. Fellows Yates
b2e043ab59
Add documentation for HOPS profile for eager @ SHH 2020-07-07 14:35:42 +02:00
James A. Fellows Yates
fcdbeaa446
Merge branch 'master' into master 2020-07-07 14:34:10 +02:00
James A. Fellows Yates
af01fccba1
Add a HOPS profile for nf-core/eager @ SHH 2020-07-07 14:31:11 +02:00
James A. Fellows Yates
7bfe43cad5
Merge pull request #169 from nf-core/shh-eager-update
Remove default non-profile bwa parameters from eager profile
2020-07-07 14:02:13 +02:00
Piotr Faba
cb7a6f756a reduce complexity 2020-07-07 13:48:28 +02:00
James A. Fellows Yates
5517d2cbe0
Remove default non-profile bwa parameters from eager profile
I realised today this is dangerous as these would not necessarily be reported if a user doesn't understand the profiles. Therefore removing these so nf-core/eager defaults are always used unless a specific profile (which would be described in the command itself) is explicitly named.
2020-07-07 13:29:13 +02:00
Piotr Faba
4181184f58 fix spaces 2020-07-02 22:00:37 +02:00
Piotr Faba
4828e78708 fix error introduced earlier 2020-07-02 21:57:44 +02:00
James A. Fellows Yates
530da4d8c0
Merge pull request #167 from jfy133/master
Bump number of eager @shh retries to account for deep sequencing data
2020-06-30 11:33:29 +02:00
James A. Fellows Yates
c52428cd72
Bump number of eager @shh retries to account for deep sequencing data 2020-06-30 08:19:25 +02:00
Alexander Peltzer
2801f25657
Merge pull request #166 from adrlar/master
Fixing an autoMounts bug for icr_davros
2020-06-26 17:52:05 +02:00
Adrian
5b890d571a adding icr_davros to list 2020-06-26 13:40:15 +01:00
Adrian
e375ad97ad reverting autoMounts due to bug 2020-06-26 13:39:37 +01:00
Phil Ewels
cd9fbb22dc
Merge pull request #161 from ewels/uct_hpc
Update UCT hex -> hpc
2020-06-22 09:18:43 +02:00
Alexander Peltzer
7774a6a8f3
Merge pull request #163 from piotr-faba-ardigen/add_bi_config
resolve  #162 bug
2020-06-19 08:57:44 +02:00
Piotr Faba
cb26bef3f3 resolve #162 bug 2020-06-18 20:30:05 +02:00
Alexander Peltzer
bb7f67e2b5
Merge pull request #160 from ewels/master
Merge czbiohub_aws_highpriority profile into czbiohub_aws
2020-06-17 19:20:07 +02:00
Phil Ewels
18a1a319ec More uct_hex references 2020-06-17 15:25:07 +02:00
Phil Ewels
29f5fa6ce4 uct_hpc docs, readme 2020-06-17 15:22:42 +02:00
Phil Ewels
53e118210f Copy over HPC config 2020-06-17 15:20:22 +02:00
Phil Ewels
dbfcd7c5e9 Rename uct_hex > uct_hpc 2020-06-17 15:17:22 +02:00
Phil Ewels
17824d2d62 Merge czbiohub_aws_highpriority profile into czbiohub_aws 2020-06-16 15:20:39 +02:00
Phil Ewels
e091ec259e
Merge pull request #158 from phue/singularity_global
CBE: don't load singularity module
2020-06-05 12:20:39 +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
adf90f3994
Merge pull request #146 from adrlar/master
Adding config for ICR davros cluster
2020-06-03 20:09:49 +02:00
Adrian
3e4db8c845 adding icr_davros to test 2020-06-03 14:55:58 +01:00
Alexander Peltzer
f877644059
Merge branch 'master' into master 2020-05-29 11:43:47 +02:00
Alexander Peltzer
0d5899eb26
Merge pull request #157 from nf-core/bi-docs
Add BI to main readme.md
2020-05-28 10:25:19 +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