Piotr Faba
3c695ba71c
test error display
2020-05-27 18:00:47 +02:00
Alexander Peltzer
6011419454
Merge pull request #154 from jfy133/master
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Update SHH nf-core/eager group-specific profiles
2020-05-27 17:52:09 +02:00
Piotr Faba
18d8edb046
add description and profile
2020-05-27 17:41:19 +02:00
Piotr Faba
66f191a1cf
declate NXF_GLOBAL_CONFIG in ci
2020-05-27 16:30:00 +02:00
Piotr Faba
2685275952
switch include off
2020-05-27 16:24:47 +02:00
Piotr Faba
c31b03108c
retry without Exception
2020-05-27 16:22:56 +02:00
Piotr Faba
1354ae4063
add bi config
2020-05-27 16:19:15 +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
e31e781f29
Remove debugging
2020-05-26 11:07:06 +02:00
Harshil Patel
5981e5ec27
Merge pull request #153 from FriederikeHanssen/cfc_scratch
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Add scratch = true to avoid writing of intermediate file to /tmp
2020-05-22 15:48:00 +01:00
James A. Fellows Yates
ff915ee504
Update shh.config
2020-05-12 12:47:59 +02:00
James A. Fellows Yates
8225e07819
Condensed base params and added names for debugging
2020-05-12 12:47:25 +02:00
James A. Fellows Yates
4814bac1c3
Fix sub-profiles
2020-05-12 12:42:42 +02:00
James A. Fellows Yates
38e9e54932
Merge pull request #151 from jfy133/master
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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
FriederikeHanssen
d6813d9c39
Add scratch = true to avoid writing of intermediate file to /tmp
2020-05-04 17:09:43 +02:00
MaxUlysse
e6f4d58fa6
update rnafusion munin specific config
2020-04-28 17:06:04 +02:00
Adrian
ad12bd4ad1
testing automounts
2020-04-28 16:03:06 +01:00
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
Adrian Larkeryd
78be4b358e
icr_davros igenomes base
2020-04-08 11:55:16 +01:00
Maxime Garcia
d1ff87a416
Merge pull request #145 from bioatlas/master
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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
ggabernet
c81f693f73
add cfc_dev config
2020-03-23 17:16:34 +01:00
Olga Botvinnik
52369ba6ad
Add AaegL5.0 config
2020-03-17 16:45:20 -07:00
Maxime Garcia
123132d89a
Update munin.config
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fix typo
2020-03-12 17:23:55 +01:00
Phil Ewels
5a3bdcca5b
Merge pull request #139 from Emiller88/utd
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fix(ganymede): use singularity/2.4.5
2020-03-11 16:54:01 +00:00
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
Edmund Miller
cece853663
fix(ganymede): use singularity/2.4.5
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Our 3.2.1 doesn't work right with snakemake or nextflow
2020-03-10 21:03:24 -05:00
Edmund Miller
c42bb07981
fix: Singularity => singularity
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For some reason ours are lowercase
2020-03-10 09:55:17 -05:00
Edmund Miller
123c44c56d
feat: add initial ganymede config
2020-03-09 16:18:41 -05:00
marcel-keller
8e3803e4d7
Update ebc.config
2020-03-09 16:57:45 +02:00
marcel-keller
c00bbe982b
Update ebc.config
2020-03-09 16:51:38 +02:00
marcel-keller
3b57519500
Update ebc.config
2020-03-09 16:48:50 +02:00
marcel-keller
de914e56ee
Create ebc.config
2020-03-09 16:08:01 +02:00
Evan Floden
d8ad376f71
Merge branch 'master' into master
2020-03-06 10:29:50 +00:00
Alexander Peltzer
59a787b179
Merge pull request #122 from marchoeppner/ccga-config
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Removing old CCGA profile from docs and linting
2020-03-06 11:17:08 +01:00
mseybold
52842de88b
Update cfc.config
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test failed, so added the the default queue
2020-03-06 10:46:37 +01:00
mseybold
8e42bbd7d0
Update cfc.config
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We just added some new HighMem nodes to the cfc, Partition/queue name is qbic, each node has 128Cores and 2TB of RAM.
The old queue (Name compute) is set to default by slurm.
Each process over 60GB of RAM or over 20cpus should run on those new nodes.
So added the queue State and adjusted the max_memory and max_cpu setting.
2020-03-06 10:25:08 +01:00
Evan Floden
8a9d3ad8a0
First commit of Google Cloud config
2020-03-06 05:47:29 +00:00
phue
e2e4dd05d3
cbe: move container cache to different filesystem
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this is a workaround for squashfs errors that occur when containers are run from beeGFS
2020-03-05 16:34:20 +01:00
Adrian Larkeryd
a67e77bb57
put comments back in correct format
2020-03-05 10:42:18 +00:00
Adrian Larkeryd
46223a3dbb
remove comments
2020-03-05 10:39:19 +00:00
Adrian Larkeryd
ead67d1e90
description and contact
2020-03-05 09:24:10 +00:00
Adrian Larkeryd
a882b6cbaa
adding icr_davros config files generic and sarek
2020-03-04 15:00:33 +00:00
James A. Fellows Yates
41a45187fa
Experiment to see if 'cleanup = true' works as expected
2020-03-03 16:47:49 +01:00
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
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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
a8d338d2aa
Merge branch 'Uppmax' of github.com:MaxUlysse/nf-core_configs into Uppmax
2020-02-24 14:37:27 +01:00
MaxUlysse
9f74e88041
update file
2020-02-24 14:36:45 +01:00
Marc Hoeppner
6c5a5c8bcb
Removing old CCGA profile from docs and linting
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Removing CCGA profile from master config
Removing CCGA profile from master config
2020-02-24 12:16:33 +01:00
Maxime Garcia
9b897345da
Update conf/pipeline/sarek/uppmax.config
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Co-Authored-By: Phil Ewels <phil.ewels@scilifelab.se>
2020-02-21 08:16:31 +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
Daniel Straub
744db30da4
Update binac.config
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This is now close to optimal I think.
2020-02-19 11:27:02 +01:00
marchoeppner
0830203b70
Adding new CCGA Med Cluster to profiles
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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
Daniel Straub
b7be65a31e
Cleanup config
2020-02-07 14:53:43 +01:00
Daniel Straub
7346bffdc8
Update binac.config
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Processes that ask for 128 Gb are queuing forever when on short queue, but executed when send to smp queue.
2020-01-28 08:48:34 +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
drpatelh
67c231d05c
Change igenomes path
2019-12-18 10:54:23 +00:00
drpatelh
089b5b8e3b
Update config
2019-12-12 13:44:37 +00:00
drpatelh
65c5668568
Update config
2019-12-12 13:02:44 +00:00
Maxime Garcia
d36172d4cf
Merge pull request #110 from MaxUlysse/MUNIN
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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
Alexander Peltzer
49cd35918a
Remove whitespace
2019-12-11 15:59:58 +01:00
Alexander Peltzer
5e6981d0ee
Export TZ in binac config
2019-12-11 15:59:25 +01:00
Alexander Peltzer
ac90acf470
Update envWhiteList for Binac Profile for testing purposes
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Add envWhitelist for TZ to fix https://github.com/nf-core/ampliseq/issues/114
2019-12-11 14:26:57 +01:00
James A. Fellows Yates
0beb98696f
Merge branch 'master' into master
2019-12-06 19:31:24 +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
James A. Fellows Yates
b28e1a0905
Wrong bracket typo fix -.-
2019-12-06 18:34:18 +01:00
Alexander Peltzer
1f7940c2ee
Merge pull request #104 from jfy133/master
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Attempt to fix process specific configs with pipeline specific configs
2019-12-06 17:16:37 +01:00
jfy133
e8b4675692
Cleanup and tweaking
2019-12-06 13:17:31 +01:00
Maxime Garcia
9497b78149
Merge pull request #100 from MaxUlysse/UPPMAX
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Improve UPPMAX configs
2019-12-06 10:52:44 +01:00
Maxime Garcia
14864bb80b
Update conf/uppmax.config
2019-12-06 10:31:56 +01:00
Alexander Peltzer
da547b4ce3
Merge pull request #102 from phue/cbe_singularity
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cbe: load singularity/3.4.1
2019-12-06 10:21:55 +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
phue
381c60e7b7
cbe: load singularity/3.4.1
2019-12-05 16:06:32 +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
MaxUlysse
f41d325873
automatic configs work on all nodes
2019-12-05 15:07:59 +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
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Condensing SHH profile(s) with sub-profiles
2019-12-05 12:51:31 +01:00
MaxUlysse
cf6e00d9f5
better match for hostname
2019-12-05 12:46:32 +01:00
MaxUlysse
20e451be3b
actually define hostname
2019-12-05 12:45:30 +01:00
MaxUlysse
0211b33a55
trying automatic configuration based on hostname
2019-12-05 12:41:18 +01:00
James A. Fellows Yates
842642a2bb
Apply suggestions from code review
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Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
2019-12-05 12:23:36 +01:00
James A. Fellows Yates
678a3841b6
Update conf/shh.config
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Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
2019-12-05 12:23:06 +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
Sabrina Krakau
2eed8f7429
Lowered max. memory for cfc
2019-11-28 12:49:02 +01:00
Olga Botvinnik
f57e00e87d
Set awsqueue parameter properly
2019-11-27 15:57:09 -08:00
Alexander Peltzer
4f77eae5cf
Mini adjustment for highmem
queue on denbi
2019-11-27 14:23:01 +01:00
Maxime Garcia
2669401a72
Merge branch 'master' into sarek
2019-11-27 13:27:43 +01:00
Alexander Peltzer
5e0e3e0567
Merge pull request #96 from jfy133/master
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Splitting SHH config to one per cluster
2019-11-27 12:06:54 +01:00
Alexander Peltzer
54719c4761
Merge pull request #95 from ggabernet/master
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Update max memory for cfc profile
2019-11-26 21:21:07 +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
88b5be3060
Merge branch 'master' of https://github.com/nf-core/configs into cbe_iGenomes
2019-11-26 18:08:43 +01:00
ggabernet
834f4b4179
updated memory cfc config
2019-11-26 17:30:41 +01:00
Alexander Peltzer
ee99d7f2d4
Merge pull request #94 from apeltzer/master
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Mini Cosmetic Fixes for README
2019-11-26 16:24:30 +01:00
Alexander Peltzer
b756ce54a4
Add genotoul fix
2019-11-26 16:09:08 +01:00
Alexander Peltzer
81739a3907
Merge pull request #93 from jfy133/master
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Updated max resources for SHH SDAG
2019-11-26 15:56:39 +01:00
James A. Fellows Yates
c3d27099ca
Updated authors
2019-11-26 15:26:05 +01:00
James A. Fellows Yates
ca6ddcadb0
Matching max CPUs to SDAG (supercruncher8)
2019-11-26 15:25:35 +01:00
MaxUlysse
6f638b7ad4
Merge branch 'sarek' of github.com:MaxUlysse/nf-core_configs into sarek
2019-11-26 15:22:02 +01:00
MaxUlysse
25f3bd68f8
container = null
2019-11-26 15:21:53 +01:00
Alexander Peltzer
5c39c1ed1a
Merge branch 'master' into master
2019-11-26 15:07:31 +01:00
Noirot Céline
611c318569
Update conf/genotoul.config
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Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
2019-11-26 14:50:05 +01:00
Noirot Céline
dd4ff452da
Update conf/genotoul.config
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Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
2019-11-26 14:49:47 +01:00
Alexander Peltzer
37c6714cc7
Nice prince
2019-11-26 14:29:52 +01:00
phue
bdf4a829b8
roll out iGenomes on cbe
2019-11-26 14:22:16 +01:00
Alexander Peltzer
23f9fd2d73
Merge branch 'master' into master
2019-11-26 14:20:36 +01:00
Maxime Garcia
68c709432f
Apply suggestions from code review
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Co-Authored-By: Phil Ewels <phil.ewels@scilifelab.se>
2019-11-26 14:17:32 +01:00
Alexander Peltzer
d592c79954
Merge branch 'master' into master
2019-11-26 13:59:06 +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
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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
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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
Maxime Garcia
93d5156c7d
Update conf/munin.config
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
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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
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rename file
improve configs
remove unnecessary params
2019-11-26 11:25:29 +01:00
Maxime Garcia
1ce8ce0c55
Apply suggestions from code review
2019-11-26 11:00:24 +01:00
MaxUlysse
75c1fd5cd9
fix tests
2019-11-26 10:43:23 +01:00