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417 commits

Author SHA1 Message Date
James A. Fellows Yates
42a1a15970
Create mpcdf.config 2020-09-03 20:11:56 +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
drpatelh
b804076959 Remove hard Singularity version 2020-08-03 11:38:10 +01:00
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
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
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
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
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
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
32ec230098
Merge pull request #156 from piotr-faba-ardigen/add_bi_config
Add bi config
2020-05-27 21:03:15 +02:00
Piotr Faba
f139750bf4 print the error message before throwing Exception 2020-05-27 19:14:43 +02:00
Piotr Faba
3c695ba71c test error display 2020-05-27 18:00:47 +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
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
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
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
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
fix typo
2020-03-12 17:23:55 +01:00
Phil Ewels
5a3bdcca5b
Merge pull request #139 from Emiller88/utd
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
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
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
Removing old CCGA profile from docs and linting
2020-03-06 11:17:08 +01:00
mseybold
52842de88b
Update cfc.config
test failed, so added the the default queue
2020-03-06 10:46:37 +01:00
mseybold
8e42bbd7d0
Update cfc.config
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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