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201 commits

Author SHA1 Message Date
James A. Fellows Yates
86566ddd3b
Merge pull request #204 from jfy133/master 
Add a 'big_data' profile for eager @ SHH
 2021-02-04 15:07:52 +01:00
James A. Fellows Yates
e32f1e46ff
Update shh.config 2021-02-04 08:13:16 +01:00
James A. Fellows Yates
c515a401c7
Update shh.config 2021-02-04 08:06:35 +01:00
James A. Fellows Yates
82fe8a04be
Update shh.config 2021-02-04 08:02:33 +01:00
James A. Fellows Yates
e7ac0bae13
Update shh.config 2021-02-04 08:00:57 +01:00
James A. Fellows Yates
eb725f9ea3
Update shh.config 2021-02-03 20:13:09 +01:00
James A. Fellows Yates
1c25cb033b
Add big_data profile 2021-01-19 13:53:01 +01:00
James A. Fellows Yates
a4c55b3ea9
Fix time limit 0-9 typo 2021-01-06 10:44:12 +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
Emelie Nilsso
febf38dd8e Removed an old process so that only relevant processes are included 2020-11-26 13:38:47 +01:00
Emelie Nilsso
d61ed01d2d Updated process names according to ampliseq main.nf 2020-11-25 17:50:30 +01:00
Emelie Nilsso
37e7cfae2c Removed unnecessary code that was used to troubleshoot 2020-11-24 07:14:23 +01:00
Emelie Nilsso
2ea06ffab8 Modified uppmax and ampliseq specific config to fit with the divided preparation of the database 2020-11-23 21:20:36 +01:00
James A. Fellows Yates
804f53c58c
Merge pull request #178 from jfy133/master 
Add Max Planck Computing and Data Facility Cobra/Raven Clusters
 2020-10-22 13:34:11 +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
James A. Fellows Yates
11f1fb71db
Update mpcdf.config 2020-09-16 10:21:58 +02:00
James A. Fellows Yates
c6f7573d01
Update mpcdf.config 2020-09-15 17:48:54 +02:00
James A. Fellows Yates
bf87ec24e7
Update mpcdf.config 2020-09-15 17:45:38 +02:00
James A. Fellows Yates
3b7902d11b
Mad multi-core increase CPUs on retry 2020-09-06 08:23:35 +02:00
James A. Fellows Yates
4335e5deb7
Update mpcdf.config 2020-09-04 20:17:09 +02:00
James A. Fellows Yates
b4e275c3b9
Add MPCDF for EAGER 2020-09-04 19:57:25 +02:00
James A. Fellows Yates
5c7ab234b6
Create mpcdf.config 2020-09-04 19:55:40 +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
57ac9257a9
Remove now deprecated EAGER flag for HOPS profile 2020-07-20 11:29:12 +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
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
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
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
f877644059
Merge branch 'master' into master 2020-05-29 11:43:47 +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
d070ed70d1
Update BWA settings based on feedback 2020-05-26 11:11:42 +02:00
James A. Fellows Yates
ff915ee504
Update shh.config 2020-05-12 12:47:59 +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
cf6e697f0b
Further update aln based on modifications of EAGER defaults 2020-05-07 09:16:08 +02:00
James A. Fellows Yates
d42d7f4146
Sets the bwa aln parameter to 0.01 which is more commonly used at SHH 2020-05-04 21:02:16 +02:00
MaxUlysse
e6f4d58fa6 update rnafusion munin specific config 2020-04-28 17:06:04 +02:00
Harshil Patel
2300d5a962
Update genomes.config 2020-04-09 18:22:41 +01:00
MaxUlysse
50a44d037b better docs and organisation of giles 2020-04-09 17:02:36 +02:00
Maxime Garcia
34dc18faf6
Update uppmax.config 2020-04-09 11:35:37 +02:00
Adrian Larkeryd
405801638a icr_davros sarek config description 2020-04-08 11:56:17 +01:00
Maxime Garcia
d1ff87a416
Merge pull request #145 from bioatlas/master 
Adding UPPMAX specific config for ampliseq
 2020-03-31 15:46:21 +02:00
Daniel Lundin
c8de9be701 Adding UPPMAX specific config for ampliseq 2020-03-31 15:17:24 +02:00
MaxUlysse
db2dd4458b Merge remote-tracking branch 'upstream/master' into UPPMAX 2020-03-30 16:41:08 +02:00
MaxUlysse
8b570507cd update s 2020-03-30 16:40:11 +02:00
Maxime Garcia
123132d89a
Update munin.config 
fix typo
 2020-03-12 17:23:55 +01:00
Maxime Garcia
b6d52fdb89
Update conf/pipeline/sarek/munin.config 2020-03-11 15:48:29 +01:00
Maxime Garcia
0f34d757a9
Update munin.config 2020-03-11 15:48:17 +01:00
MaxUlysse
d24a296a01 add munin/rnafusion specific config 2020-03-11 14:02:01 +01:00
MaxUlysse
dd1ddf864b update sarek munin config 2020-03-11 14:01:28 +01:00
Adrian Larkeryd
a882b6cbaa adding icr_davros config files generic and sarek 2020-03-04 15:00:33 +00:00
Maxime Garcia
9a8bb12020
Update conf/pipeline/sarek/uppmax.config 2020-02-27 17:22:03 +01:00
Maxime Garcia
8acbdacf03
Update conf/pipeline/sarek/uppmax.config 
Co-Authored-By: Johannes Alneberg <johannes.alneberg@scilifelab.se>
 2020-02-27 17:21:03 +01:00
Maxime Garcia
09ff8f5790
Update conf/pipeline/sarek/uppmax.config 2020-02-27 17:02:31 +01:00
Maxime Garcia
17d6a7e922
Update conf/pipeline/sarek/uppmax.config 2020-02-27 17:02:13 +01:00
Maxime Garcia
ab8998e12b
Update uppmax.config 2020-02-27 16:52:51 +01:00
MaxUlysse
9f74e88041 update file 2020-02-24 14:36:45 +01:00
MaxUlysse
aa905cd645 add UPPMAX specific sarek config 2020-02-20 17:14:18 +01:00
James A. Fellows Yates
638758423a
Restricts MALT re-tries and hardcodes resources so cannot go above SDAG max 2019-12-21 20:55:54 +01:00
Maxime Garcia
d36172d4cf
Merge pull request #110 from MaxUlysse/MUNIN 
fix issue with withLabel selector
 2019-12-12 13:03:23 +01:00
MaxUlysse
2bf66514c5 fix issue with withLabel selector 2019-12-12 11:50:10 +01:00
Alexander Peltzer
a6d08ed646
Adjust custom pipeline config for ampliseq on BINAC 2019-12-11 16:09:44 +01:00
James A. Fellows Yates
8747be8120
More tweaks, nextflow appears to add a little extra? 2019-12-06 19:27:16 +01:00
James A. Fellows Yates
5c6760b2f0
Tweak back again 2019-12-06 19:25:07 +01:00
James A. Fellows Yates
46f6d20a77
Put parameters back to correct levels 2019-12-06 19:13:29 +01:00
James A. Fellows Yates
18931763fa
Add space? 2019-12-06 19:11:08 +01:00
James A. Fellows Yates
f59443daf0
Update shh.config 2019-12-06 19:09:20 +01:00
James A. Fellows Yates
1ab1370872
Try to make resources satisfiable 2019-12-06 19:06:05 +01:00
James A. Fellows Yates
6e596d1730
Fix stupid wrong bracket typo -.- 2019-12-06 18:37:39 +01:00
jfy133
e8b4675692 Cleanup and tweaking 2019-12-06 13:17:31 +01:00
James A. Fellows Yates
0033b74e4e
Update shh.config 2019-12-05 18:08:39 +01:00
James A. Fellows Yates
dc0f1dfb40
Update shh.config 2019-12-05 17:58:49 +01:00
James A. Fellows Yates
b1a8b45aa0
Maybe typo? 2019-12-05 17:52:53 +01:00
jfy133
731372dac2 Added SHH specific EAGER configuration 2019-12-05 17:01:10 +01:00
MaxUlysse
25f3bd68f8 container = null 2019-11-26 15:21:53 +01:00
MaxUlysse
ebdfc2a768 fix container/module collision 2019-11-26 11:59:00 +01:00
Maxime Garcia
880551d246 Apply suggestions from code review 2019-11-26 11:58:13 +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
Maxime Garcia
9d23f7a266 Update conf/pipeline/sarek/munin.config 2019-11-26 11:56:02 +01:00
MaxUlysse
45cec1ac2f Add specific sarek config base, munin specific sarek config and docs 
rename file

improve configs

remove unnecessary params
 2019-11-26 11:52:53 +01:00
MaxUlysse
028008c1d0 improve syntax 2019-11-26 11:48:29 +01:00
MaxUlysse
e98f74e47b actually belong to nf-core/configs/munin 2019-11-26 11:48:29 +01:00
MaxUlysse
edde1ee64d fix container/module collision 2019-11-26 11:48:29 +01:00
Maxime Garcia
9a57e487d7 Apply suggestions from code review 2019-11-26 11:48:29 +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
Maxime Garcia
73047968cf Update conf/pipeline/sarek/munin.config 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