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474 commits

Author SHA1 Message Date
James A. Fellows Yates
832edaa450
Merge branch 'master' into eva 2021-04-06 17:51:46 +02:00
James Fellows Yates
be1d35840d Add EVA and EAGER@EVA 2021-04-06 17:48:16 +02:00
James Fellows Yates
d69af0f287 Merging 2021-04-06 16:42:22 +02:00
phue
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
6e201a71f4
ATAC-seq pipeline config
Java processes with overhead memory requirements
2021-03-30 16:31:00 +01:00
ameynert
e5f2a63079
Java overhead processes list updated
Added all processes calling GATK for Mutect2 variant calling
2021-03-30 16:21:53 +01:00
ameynert
adfb5366b9
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
8fc60e2e70 add config for biohpc_gen 2021-03-29 19:25:58 +02:00
Gisela Gabernet
71a97ba316
Merge pull request #185 from ggabernet/master
awsbatch config update
2021-03-28 20:59:40 +02:00
Phil Ewels
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
26b5904df1
Merge pull request #218 from asafpr/master
added jax singularity cache dir
2021-03-24 17:39:03 +01:00
Asaf Peer
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
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