James A. Fellows Yates
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756f067213
|
Merge pull request #248 from jfy133/eva
Fix MakeSeqDict eager @ eva
|
2021-06-07 13:26:05 +02:00 |
|
James A. Fellows Yates
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da8e002969
|
Merge pull request #247 from jfy133/shh-fx
Fix eageR@SHH HOPS profile human ref path
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2021-06-07 10:55:01 +02:00 |
|
James A. Fellows Yates
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fc8b1162c1
|
Fix HOPS huamn ref path
|
2021-06-07 10:48:35 +02:00 |
|
James A. Fellows Yates
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5bf57894a5
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Merge pull request #246 from jfy133/shh-update
Make eager@SHH big_data go by default to medium via run time
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2021-06-04 12:32:28 +02:00 |
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James A. Fellows Yates
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31d46cb0a9
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Make big_data go by default to medium via run time
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2021-06-04 12:22:54 +02:00 |
|
Øyvind Almelid
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c75ceec35d
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Merge pull request #244 from oalmelid/master
eddie.conf: Add TMPDIR and mount for it to singularity configuration + Migrate to BioinformaticsResources for genomes.
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2021-05-25 10:03:05 +01:00 |
|
Øyvind Almelid
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f6578f727d
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Add TMPDIR and mount for it to singularity configuration
|
2021-05-25 09:54:08 +01:00 |
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Olga Botvinnik
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2ac4693421
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Merge pull request #243 from nf-core/olgabot-patch-1
executor.cli --> aws.batch.cliPath
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2021-05-20 10:34:55 -07:00 |
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MaxUlysse
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05548bdb75
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fix: forgotten }
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2021-05-20 09:37:48 +02:00 |
|
Olga Botvinnik
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8166e0f606
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executor.cli --> aws.batch.cliPath
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2021-05-19 13:36:15 -07:00 |
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MaxUlysse
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73fcc4495a
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feat: update owner of profile
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2021-05-19 20:46:52 +02:00 |
|
Phil Ewels
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9c4830c8d5
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Merge pull request #238 from nf-core/hebbe-config-fix
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2021-05-19 17:46:52 +02:00 |
|
James A. Fellows Yates
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3bcd55966d
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Update eva.config
|
2021-05-05 11:39:33 +02:00 |
|
James A. Fellows Yates
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f2413553a3
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Merge pull request #240 from jfy133/shh
eager@SHH Add additional retry allowance for silly big data in markdups
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2021-05-05 10:52:58 +02:00 |
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James A. Fellows Yates
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a849fe991c
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Add additional retry allowance for silly big data in markdups
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2021-05-04 21:43:19 +02:00 |
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Maxime U. Garcia
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77bd7f567f
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Merge pull request #228 from asafpr/master
updated jax resources
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2021-05-02 14:47:19 +02:00 |
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Phil Ewels
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76b62b478d
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Fix hebbe withName regex
|
2021-04-29 23:06:56 +02:00 |
|
Barry digby
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24a4119e43
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memory test
|
2021-04-29 14:24:57 +01:00 |
|
Barry digby
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aeb0346cce
|
.
|
2021-04-28 20:14:32 +01:00 |
|
Barry digby
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8340e89768
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nuig.config first commit
|
2021-04-28 17:28:01 +01:00 |
|
Alexander Peltzer
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c12c373969
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Merge pull request #235 from aunderwo/cambridge
Add Cambridge University HPC config
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2021-04-25 10:40:56 +02:00 |
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Gisela Gabernet
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4e9e5d2c67
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Merge branch 'master' into cfc_sarek
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2021-04-23 16:47:04 +02:00 |
|
Anthony Underwood
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8b3951b244
|
Create cambridge.config
|
2021-04-22 16:00:37 +01:00 |
|
Anthony Underwood
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351c5773f0
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Add queue limits for 'normal'
|
2021-04-22 11:59:34 +01:00 |
|
Anthony Underwood
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7d8770af1a
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Create sanger.config
|
2021-04-21 16:39:55 +01:00 |
|
phue
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b225a0555a
|
biohpc_gen: update software tree path
|
2021-04-21 10:08:00 +02:00 |
|
James A. Fellows Yates
|
eacdf89e53
|
Update eva.config
|
2021-04-20 13:17:35 +02:00 |
|
James A. Fellows Yates
|
b9a00f7926
|
Update mpcdf.config
|
2021-04-15 22:27:07 +02:00 |
|
Harshil Patel
|
7ac66dcd72
|
Update crick.config
|
2021-04-13 17:07:02 +01:00 |
|
Combiz Khozoie
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c571c05ab9
|
Merge pull request #219 from slacalle/patch-2
Imperial College | Remove "/rdsgpfs"
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2021-04-13 15:28:00 +01:00 |
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MaxUlysse
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3918e0aa9d
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feat: remove kraken profile
|
2021-04-13 15:14:14 +02:00 |
|
Asaf Peer
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a0c8a9ec8f
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updated jax resources
|
2021-04-12 16:00:34 -04:00 |
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Phil Ewels
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2f77d16b70
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Merge pull request #220 from ewels/master
UPPMAX: Avoid undefined parameter warnings
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2021-04-08 15:06:00 +02:00 |
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James A. Fellows Yates
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161c3a33d4
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Merge branch 'master' into eva
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2021-04-07 19:28:16 +02:00 |
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James A. Fellows Yates
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ce465cca57
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Apply suggestions from code review
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
|
2021-04-07 19:27:24 +02:00 |
|
Alexander Peltzer
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91f50aad4e
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Merge pull request #221 from phue/biohpc_gen
Add BioHPC Genomics config
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2021-04-07 14:03:22 +02:00 |
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ameynert
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0ab9edde72
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Delete conf/pipeline/atacseq directory
Pipeline-specific config not supported yet by ATAC-seq pipeline
|
2021-04-07 09:24:30 +01:00 |
|
James A. Fellows Yates
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832edaa450
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Merge branch 'master' into eva
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2021-04-06 17:51:46 +02:00 |
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James Fellows Yates
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be1d35840d
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Add EVA and EAGER@EVA
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2021-04-06 17:48:16 +02:00 |
|
James Fellows Yates
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d69af0f287
|
Merging
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2021-04-06 16:42:22 +02:00 |
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phue
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60ae267e43
|
use SLURM_CLUSTERS env var
this seems to be more reliable for queue checking than using the clusterOptions directive. See https://github.com/nextflow-io/nextflow/issues/807
|
2021-04-06 11:35:01 +02:00 |
|
ameynert
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6e201a71f4
|
ATAC-seq pipeline config
Java processes with overhead memory requirements
|
2021-03-30 16:31:00 +01:00 |
|
ameynert
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e5f2a63079
|
Java overhead processes list updated
Added all processes calling GATK for Mutect2 variant calling
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2021-03-30 16:21:53 +01:00 |
|
ameynert
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adfb5366b9
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Java overhead process list updated
Added HaplotypeCaller and GenotypeGVCFs to set of processes that need Java overhead
|
2021-03-30 16:15:17 +01:00 |
|
phue
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8fc60e2e70
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add config for biohpc_gen
|
2021-03-29 19:25:58 +02:00 |
|
Gisela Gabernet
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71a97ba316
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Merge pull request #185 from ggabernet/master
awsbatch config update
|
2021-03-28 20:59:40 +02:00 |
|
Phil Ewels
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d34bc40841
|
UPPMAX: add to schema_ignore_params
|
2021-03-26 15:22:57 +01:00 |
|
Phil Ewels
|
eccc9ea8d5
|
Define params.project and params.clusterOptions in uppmax config
|
2021-03-26 15:20:32 +01:00 |
|
Santiago Lacalle
|
e2c583d558
|
Remove "/rdsgpfs"
"/rdsgpfs" symlink will not be present on all nodes. Without that mount the container creation will fail.
|
2021-03-25 12:38:15 +00:00 |
|
Alexander Peltzer
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26b5904df1
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Merge pull request #218 from asafpr/master
added jax singularity cache dir
|
2021-03-24 17:39:03 +01:00 |
|
Asaf Peer
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922ab87eb0
|
added jax singularity cache dir
|
2021-03-24 11:25:47 -04:00 |
|
Phil Ewels
|
bfab371c94
|
Merge branch 'master' into master
|
2021-03-24 12:36:15 +01:00 |
|
ameyner2
|
da8cf2f207
|
Added pipeline-specific config files for rnaseq and sarek
|
2021-03-24 10:46:26 +00:00 |
|
Asaf Peer
|
9b2d5bfead
|
Merge pull request #216 from asafpr/master
Added JAX conf
|
2021-03-24 03:31:14 -04:00 |
|
Alexander Peltzer
|
5988c51361
|
Merge pull request #211 from DoaneAS/master
Adding WCM.config for Weill Cornell Medicine cluster
|
2021-03-23 14:58:27 +01:00 |
|
Edmund Miller
|
a6975cdd4e
|
fix(ganymede): large => high
Co-authored-by: drpatelh <drpatelh@users.noreply.github.com>
|
2021-03-22 12:42:56 -05:00 |
|
Edmund Miller
|
34ccce9531
|
fix(ganymede): Add process resources
Trimgalore though it can be a bottom neck, doesn't require the 1 big
memory node we have and can be run on the genomics queue.
|
2021-03-21 21:47:59 -05:00 |
|
Edmund Miller
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4570718b12
|
fix(ganymede): Add TMPDIR and SINGULARITY_CACHEDIR env variables
|
2021-03-21 21:45:39 -05:00 |
|
Asaf Peer
|
30c864e112
|
added JAX conf
|
2021-03-21 06:49:11 -04:00 |
|
ameyner2
|
059d353a1e
|
Removed Conda, added automount Singularity
|
2021-03-18 12:31:56 +00:00 |
|
Rike
|
6221b67bcf
|
Give Strelka a complete compute node
|
2021-03-18 11:11:02 +01:00 |
|
Rike
|
b1846af9d3
|
reduce mapping resource further to compute node
|
2021-03-18 11:10:00 +01:00 |
|
FriederikeHanssen
|
67c93a4743
|
Update conf/pipeline/sarek/cfc.config
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
|
2021-03-18 11:06:38 +01:00 |
|
Rike
|
b70097e495
|
remove new line
|
2021-03-17 15:46:18 +01:00 |
|
ameyner2
|
d4cd07c646
|
Typo in beforescript
|
2021-03-17 09:21:26 +00:00 |
|
Noirot Céline
|
7e9f83ee81
|
Add IFB config
|
2021-03-16 15:54:19 +01:00 |
|
ameyner2
|
cfe13fe6c1
|
Fixed typo & added singularity tmpdir
|
2021-03-15 15:42:30 +00:00 |
|
Ashley S Doane
|
e7f8189dfc
|
Create wcm.config
|
2021-03-11 13:52:11 -05:00 |
|
Rike
|
bb124a9be8
|
Reduce vc to run on compute
|
2021-03-11 16:11:41 +01:00 |
|
FriederikeHanssen
|
79ddbe1fea
|
Add missing bracket
|
2021-03-11 09:29:03 +01:00 |
|
FriederikeHanssen
|
0057132e02
|
remove check_reource statement
|
2021-03-11 09:27:08 +01:00 |
|
phue
|
da3bd2693d
|
cbe: add rapid qos
and update config url
|
2021-03-10 11:26:01 +01:00 |
|
FriederikeHanssen
|
eb9012919c
|
Set values for processes with max_mem/max_cpus
|
2021-03-10 11:16:18 +01:00 |
|
Graeme Grimes
|
babeccd020
|
changed # to // for comments
|
2021-03-04 16:45:21 +00:00 |
|
ameynert
|
6f09a233f0
|
Added singularity module
|
2021-03-04 14:46:23 +00:00 |
|
ameynert
|
3af2c6409f
|
Initial commit of eddie.config
|
2021-03-03 09:59:16 +00:00 |
|
maxibor
|
286e18b80c
|
update shh config after CDAG departure
|
2021-02-17 10:22:05 +01:00 |
|
drpatelh
|
01a4f8559e
|
Update links to be consistent
|
2021-02-16 13:17:16 +00:00 |
|
Harshil Patel
|
6ffaf922c5
|
Update genomes.config
|
2021-02-16 10:28:32 +00:00 |
|
Marc Hoeppner
|
1f2fce00aa
|
Updating the CCGA DX profile to new storage system
|
2021-02-16 09:02:16 +01:00 |
|
Harshil Patel
|
4de0855218
|
Update genomes.config
|
2021-02-15 18:48:03 +00:00 |
|
drpatelh
|
9d500cf679
|
Reorder params
|
2021-02-15 17:02:26 +00:00 |
|
drpatelh
|
f283dfb2dc
|
Add ARTIC primer sets to genome config
|
2021-02-15 16:58:30 +00:00 |
|
James Fellows Yates
|
537f52a640
|
Add MPI-EVA profile
|
2021-02-14 17:50:20 +01:00 |
|
ggabernet
|
9b5bcbd434
|
update aws clipath
|
2021-02-09 22:06:59 +01:00 |
|
ggabernet
|
0909708b97
|
update with upstream
|
2021-02-09 22:01:27 +01:00 |
|
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 |
|
Charles Plessy
|
1608b36dcf
|
Institutional profile for Okinawa Institute of Science and Technology
|
2021-02-02 17:40:10 +09:00 |
|
Thiseas C. Lamnidis
|
713a032a36
|
Add debug profile
which deactivates cleanup of workdir after successful run
|
2021-01-26 15:08:21 +01:00 |
|
James A. Fellows Yates
|
26d164ca74
|
Remove ceh profile for now
|
2021-01-21 13:15:08 +01:00 |
|
Åshild J. Vågene
|
594985f1ee
|
Update and rename ceh.config to seg_globe.config
|
2021-01-21 11:43:34 +01:00 |
|
Åshild J. Vågene
|
8fa720b9cc
|
Update conf/ceh.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2021-01-21 11:15:06 +01:00 |
|
Åshild J. Vågene
|
f8973f153a
|
Update ceh.config
|
2021-01-21 00:31:49 +01:00 |
|
Åshild J. Vågene
|
91594dffea
|
Update ceh.config
|
2021-01-21 00:29:43 +01:00 |
|
Åshild J. Vågene
|
c11c26f15f
|
Create ceh.config
|
2021-01-20 23:45:26 +01:00 |
|
James A. Fellows Yates
|
1c25cb033b
|
Add big_data profile
|
2021-01-19 13:53:01 +01:00 |
|
rbpisupati
|
9b5ac5c89d
|
added anaconda module for cbe
|
2021-01-15 12:55:46 +01:00 |
|
James A. Fellows Yates
|
a4c55b3ea9
|
Fix time limit 0-9 typo
|
2021-01-06 10:44:12 +01:00 |
|
Combiz Khozoie
|
17cf4e3b35
|
fixed indents
|
2020-12-18 15:34:56 +00:00 |
|
Combiz Khozoie
|
3824403b4e
|
removed workDir from Imperial configs
|
2020-12-18 10:31:36 +00:00 |
|
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 |
|
marcel-keller
|
c9ceaff3b3
|
change of directory for conda environments
change of directory due to recent changes in our infrastructure
|
2020-12-09 15:11:21 +02:00 |
|
emnilsson
|
8cc2fc5ecb
|
Merge pull request #193 from emnilsson/master
Modified ampliseq-specific uppmax-config
|
2020-12-02 13:40:43 +01:00 |
|
Alexander Peltzer
|
99985c658f
|
Merge pull request #194 from marcel-keller/ebc
Update ebc.config
|
2020-11-26 14:12:33 +01:00 |
|
marcel-keller
|
5590a9743a
|
Update ebc.config
queueSize to 64
|
2020-11-26 15:05:25 +02:00 |
|
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
|
cd59bba83e
|
Merge branch 'master' of https://github.com/nf-core/configs
|
2020-11-24 07:10:05 +01:00 |
|
Emelie Nilsso
|
c47088cda2
|
Merge remote-tracking branch 'origin'
|
2020-11-23 21:34:08 +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 |
|
Thiseas C. Lamnidis
|
71d1ff2226
|
Add params block to sdag queue
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2020-11-18 13:04:46 +01:00 |
|
Thiseas C. Lamnidis
|
da781907f2
|
Move sdag queue specification block in sdag profile
|
2020-11-17 19:45:06 +01:00 |
|
Maxime Borry
|
c95fd9d52f
|
Merge pull request #186 from jfy133/shh-singularity-runoptions
Remove custom singularity runOptions from SHH config
|
2020-11-10 15:39:40 +01:00 |
|
James A. Fellows Yates
|
9d4d682867
|
Update shh.config
|
2020-11-10 15:14:03 +01:00 |
|
Gisela Gabernet Garriga
|
885f0ce5f6
|
awsbatch config update
|
2020-11-09 22:41:38 +01:00 |
|
lecorguille
|
90d1f9072b
|
Add ABiMS - autoMounts = false
|
2020-10-22 18:18:55 +02:00 |
|
lecorguille
|
a63ca751ee
|
Add ABiMS
|
2020-10-22 16:57:41 +02:00 |
|
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 |
|
James A. Fellows Yates
|
3995057d7f
|
Update mpcdf.config
|
2020-10-22 10:42:46 +02:00 |
|
James A. Fellows Yates
|
05deeca2d6
|
Update mpcdf.config
|
2020-10-15 14:22:35 +02:00 |
|
James A. Fellows Yates
|
e26c22b2f1
|
Update shh.config
|
2020-09-29 14:03:35 +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 |
|
James A. Fellows Yates
|
11f1fb71db
|
Update mpcdf.config
|
2020-09-16 10:21:58 +02:00 |
|
James A. Fellows Yates
|
bbbdd3cb0f
|
Update mpcdf.config
|
2020-09-16 10:21:42 +02:00 |
|
James A. Fellows Yates
|
5b3492d240
|
Update mpcdf.config
|
2020-09-16 10:21:26 +02:00 |
|
James A. Fellows Yates
|
3115963b3e
|
Update mpcdf.config
|
2020-09-15 19:53:27 +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 |
|
Edmund Miller
|
2c06019d89
|
fix(utd): Add check for less than 12 cpu
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2020-09-13 20:46:14 -05:00 |
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Edmund Miller
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dc2735207e
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feat(utd): add Kim queue
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2020-09-13 20:46:10 -05:00 |
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James A. Fellows Yates
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3b7902d11b
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Mad multi-core increase CPUs on retry
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2020-09-06 08:23:35 +02:00 |
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James A. Fellows Yates
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4335e5deb7
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Update mpcdf.config
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2020-09-04 20:17:09 +02:00 |
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James A. Fellows Yates
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b4e275c3b9
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Add MPCDF for EAGER
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2020-09-04 19:57:25 +02:00 |
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James A. Fellows Yates
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5c7ab234b6
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Create mpcdf.config
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2020-09-04 19:55:40 +02:00 |
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James A. Fellows Yates
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0a685c1cc2
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Update mpcdf.config
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2020-09-03 20:24:11 +02:00 |
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James A. Fellows Yates
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42a1a15970
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Create mpcdf.config
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2020-09-03 20:11:56 +02:00 |
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James A. Fellows Yates
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c3fa87e4bc
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Add microbiome screening profile for NT sized MALT runs for nf-core/eager@SHH
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2020-08-11 09:18:36 +02:00 |
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drpatelh
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b804076959
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Remove hard Singularity version
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2020-08-03 11:38:10 +01:00 |
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maxibor
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69a0bd572b
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add temporary CDAG setting for SHH config
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2020-07-23 15:38:28 +02:00 |
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James A. Fellows Yates
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d38ffc289b
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Merge pull request #173 from jfy133/shh-eager-hops-update
Remove now deprecated EAGER flag for HOPS profile
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2020-07-20 11:34:49 +02:00 |
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James A. Fellows Yates
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57ac9257a9
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Remove now deprecated EAGER flag for HOPS profile
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2020-07-20 11:29:12 +02:00 |
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