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Author SHA1 Message Date
Olga Botvinnik
561dd6b8bb
Delete czbiohub_aws.config 2020-09-30 11:30:02 -07:00
Olga Botvinnik
9202ac7e01
Update main.yml 2020-09-29 16:22:09 -07:00
Olga Botvinnik
b1bd038a11
Update conf/czbiohub_local.config 
Co-authored-by: Phoenix Logan <phoenix@phoenixlogan.net>
 2020-09-29 16:20:16 -07:00
Olga Botvinnik
922638be0a
Update nfcore_custom.config 2020-09-29 16:17:31 -07:00
Olga Botvinnik
2c290d5171
Create czbiohub_local.config 2020-09-29 16:16:41 -07:00
James A. Fellows Yates
2c2d23ac26
Merge pull request #181 from nf-core/shh-patch 
Update SHH profile to reduce number of parallel jobs
 2020-09-29 14:24:12 +02:00
James A. Fellows Yates
e26c22b2f1
Update shh.config 2020-09-29 14:03:35 +02:00
Johannes Alneberg
59cd8d69ed
Merge pull request #180 from MaxUlysse/rackham 
Rackham
 2020-09-29 10:31:04 +02:00
MaxUlysse
2ccbdd3367 update params to latest version 2020-09-28 13:59:42 +02:00
MaxUlysse
8c0cc4b9ec code polishing 2020-09-25 09:57:50 +02:00
MaxUlysse
81f910cc95 add specific BamQC config 2020-09-25 09:49:43 +02:00
MaxUlysse
fbe7bd133a update uppmax specific sarek config 2020-09-25 08:33:53 +02:00
Edmund Miller
87c757dc47
Merge pull request #179 from Emiller88/utd 
feat: add Kim queue
 2020-09-14 10:28:43 -05:00
Edmund Miller
2c06019d89
fix(utd): Add check for less than 12 cpu 2020-09-13 20:46:14 -05:00
Edmund Miller
dc2735207e
feat(utd): add Kim queue 2020-09-13 20:46:10 -05:00
James A. Fellows Yates
3d744d9aea
Merge pull request #176 from jfy133/master 
Add new group profile for eager@SHH
 2020-08-11 09:24:43 +02:00
James A. Fellows Yates
09cfabd37f
Add new microbiome_screening profile to docs 2020-08-11 09:20:31 +02:00
James A. Fellows Yates
c3fa87e4bc
Add microbiome screening profile for NT sized MALT runs for nf-core/eager@SHH 2020-08-11 09:18:36 +02:00
James A. Fellows Yates
de9f5ab560
Merge pull request #11 from nf-core/master 
Get latest changes
 2020-08-11 09:10:13 +02:00
Harshil Patel
69a660da3b
Merge pull request #175 from drpatelh/master 
Remove loading of specific Singularity version
 2020-08-03 11:46:21 +01:00
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