Rogan Grant
09e0ea2674
typo
2021-07-28 13:46:40 -05:00
Rogan Grant
e1e0810d1b
Clean up module loading script
2021-07-28 13:44:48 -05:00
Rogan Grant
e2c566ed13
Testing "automounts"
2021-07-28 13:38:06 -05:00
Rogan Grant
f104250ff4
Removed comment
2021-07-28 13:34:49 -05:00
Rogan Grant
9df267a192
Merged duplicate params
2021-07-28 13:27:17 -05:00
Rogan Grant
ff6823ec1d
removed unnecessary space
2021-07-28 13:22:52 -05:00
Rogan Grant
9957e9eea1
Version 1 of custom config with queue-switching for long jobs and module loading
2021-07-28 13:11:02 -05:00
Barry digby
70b2644c9a
.
2021-07-27 17:39:37 +01:00
Barry digby
2b6e80561a
Merge branch 'master' of https://github.com/nf-core/configs into
2021-07-27 17:13:17 +01:00
Barry digby
4f962260d0
s
2021-07-27 17:08:53 +01:00
Barry digby
04c0da5a2f
nuig confg (lugh)
2021-07-27 17:05:27 +01:00
ameynert
2112168420
Set BLASTDB_LMDB_MAP_SIZE
...
This environment variable needs to be set in order to prevent memory allocation errors in the MAKEBLASTDB process.
2021-07-22 15:07:19 +01:00
ameynert
4ceb369af5
eddie.config for viralrecon pipeline
2021-07-21 12:10:43 +01:00
Maxime U. Garcia
30e058abf0
Merge branch 'master' into master_kraken
2021-07-20 09:26:56 +02:00
Harshil Patel
962dca7a46
Add ARTIC v1200 primers to genomes config for viralrecon
2021-07-12 12:24:49 +01:00
Gisela Gabernet
e2088a008d
Merge branch 'master' into master
2021-07-03 12:24:42 +02:00
ggabernet
ee2e8392ab
add aws_tower profile
2021-07-03 12:17:21 +02:00
Harshil Patel
69f63a006d
Merge pull request #254 from drpatelh/articv4
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Add ARTIC v4 primers to genomes config for viralrecon
2021-07-01 12:31:02 +01:00
Gisela Gabernet
aae0f0bf07
Merge pull request #255 from ggabernet/master
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update cfc configs
2021-07-01 10:59:25 +02:00
ggabernet
d59d099fe8
remove load module in cfc configs
2021-07-01 10:52:54 +02:00
James A. Fellows Yates
5f4b915ae8
Update eva.config
2021-06-29 11:31:00 +02:00
Harshil Patel
93cfc48afd
Add ARTIC v4 primers to genomes config
2021-06-21 21:04:16 +01:00
Edmund Miller
21e1037e0c
docs(sysbio): Add rnaseq specific docs
2021-06-17 09:18:45 -05:00
Edmund Miller
e35c5fd1d8
fix(sysbio): Add nf-core params
2021-06-17 08:32:31 -05:00
Edmund Miller
41ae99d34a
feat(sysbio): Add cleanup
2021-06-17 08:17:55 -05:00
Edmund Miller
14a2106c63
fix(sysbio): Move rnaseq specific things to pipeline config
2021-06-17 08:14:48 -05:00
phue
45213cf6db
add note about upcoming upstream fix
...
also refactor the closure to make it slightly more readable
2021-06-17 11:12:36 +02:00
Edmund Miller
472082254a
fix(sysbio): Add Star resources
2021-06-16 21:18:48 -05:00
Edmund Miller
b11f137901
fix(sysbio): Leave igenomes unfinished
2021-06-16 21:18:28 -05:00
Edmund Miller
04d0b27e81
fix(sysbio): Reduce memory on high processes
2021-06-16 21:17:40 -05:00
phue
f5c36dde3e
cbe: send SIGUSR2 upon job termination
...
Previously, if a process hit the walltime limit and received SIGKILL
from the slurm scheduler, singularity did not properly propagate such
(soft) kill signal. This prevented the exit code to be caught, e.g for
resubmission purposes.
This commit introduces a workaround using slurms --signal directive
to send SIGUSR2 to the singularity process itself (instead of
container child processes, which presumably was happening before).
Effectively, once a job reaches walltime limit, this will result in
exitcode 140 which is typically caught by the errorStrategy in nf-core
pipelines
See also:
https://slurm.schedmd.com/sbatch.html#OPT_signal
https://github.com/nextflow-io/nextflow/issues/2163
https://github.com/nextflow-io/nextflow/issues/1561
2021-06-16 16:36:39 +02:00
Edmund Miller
2b58a62a9b
feat(utd): Add initial sysbio config
2021-06-11 14:50:58 -05:00
ggabernet
c3385593cb
revert cfc config
2021-06-11 14:59:09 +02:00
mseybold
f196de8246
Update cfc.config
...
singularity is now installed natively on the nodes, so no more need for a module here
2021-06-10 12:34:58 +02:00
James A. Fellows Yates
756f067213
Merge pull request #248 from jfy133/eva
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Fix MakeSeqDict eager @ eva
2021-06-07 13:26:05 +02:00
James A. Fellows Yates
da8e002969
Merge pull request #247 from jfy133/shh-fx
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Fix eageR@SHH HOPS profile human ref path
2021-06-07 10:55:01 +02:00
James A. Fellows Yates
fc8b1162c1
Fix HOPS huamn ref path
2021-06-07 10:48:35 +02:00
James A. Fellows Yates
5bf57894a5
Merge pull request #246 from jfy133/shh-update
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Make eager@SHH big_data go by default to medium via run time
2021-06-04 12:32:28 +02:00
James A. Fellows Yates
31d46cb0a9
Make big_data go by default to medium via run time
2021-06-04 12:22:54 +02:00
Øyvind Almelid
c75ceec35d
Merge pull request #244 from oalmelid/master
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eddie.conf: Add TMPDIR and mount for it to singularity configuration + Migrate to BioinformaticsResources for genomes.
2021-05-25 10:03:05 +01:00
Øyvind Almelid
f6578f727d
Add TMPDIR and mount for it to singularity configuration
2021-05-25 09:54:08 +01:00
Olga Botvinnik
2ac4693421
Merge pull request #243 from nf-core/olgabot-patch-1
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executor.cli --> aws.batch.cliPath
2021-05-20 10:34:55 -07:00
MaxUlysse
05548bdb75
fix: forgotten }
2021-05-20 09:37:48 +02:00
Olga Botvinnik
8166e0f606
executor.cli --> aws.batch.cliPath
2021-05-19 13:36:15 -07:00
MaxUlysse
73fcc4495a
feat: update owner of profile
2021-05-19 20:46:52 +02:00
Phil Ewels
9c4830c8d5
Merge pull request #238 from nf-core/hebbe-config-fix
2021-05-19 17:46:52 +02:00
James A. Fellows Yates
3bcd55966d
Update eva.config
2021-05-05 11:39:33 +02:00
James A. Fellows Yates
f2413553a3
Merge pull request #240 from jfy133/shh
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eager@SHH Add additional retry allowance for silly big data in markdups
2021-05-05 10:52:58 +02:00
James A. Fellows Yates
a849fe991c
Add additional retry allowance for silly big data in markdups
2021-05-04 21:43:19 +02:00
Maxime U. Garcia
77bd7f567f
Merge pull request #228 from asafpr/master
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updated jax resources
2021-05-02 14:47:19 +02:00
Phil Ewels
76b62b478d
Fix hebbe withName regex
2021-04-29 23:06:56 +02:00
Barry digby
24a4119e43
memory test
2021-04-29 14:24:57 +01:00
Barry digby
aeb0346cce
.
2021-04-28 20:14:32 +01:00
Barry digby
8340e89768
nuig.config first commit
2021-04-28 17:28:01 +01:00
Alexander Peltzer
c12c373969
Merge pull request #235 from aunderwo/cambridge
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Add Cambridge University HPC config
2021-04-25 10:40:56 +02:00
Gisela Gabernet
4e9e5d2c67
Merge branch 'master' into cfc_sarek
2021-04-23 16:47:04 +02:00
Anthony Underwood
8b3951b244
Create cambridge.config
2021-04-22 16:00:37 +01:00
Anthony Underwood
351c5773f0
Add queue limits for 'normal'
2021-04-22 11:59:34 +01:00
Anthony Underwood
7d8770af1a
Create sanger.config
2021-04-21 16:39:55 +01:00
phue
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
c571c05ab9
Merge pull request #219 from slacalle/patch-2
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Imperial College | Remove "/rdsgpfs"
2021-04-13 15:28:00 +01:00
MaxUlysse
3918e0aa9d
feat: remove kraken profile
2021-04-13 15:14:14 +02:00
Asaf Peer
a0c8a9ec8f
updated jax resources
2021-04-12 16:00:34 -04:00
Pontus Freyhult
ff20f121f9
Support use of very fat node in snowy
2021-04-12 19:34:28 +02:00
Pontus Freyhult
0987cbe1be
Better test for snowy
2021-04-12 19:32:21 +02:00
Pontus Freyhult
7be4279718
Handle different (unexpected) sinfo returns in different cases
2021-04-12 19:31:41 +02:00
Pontus Freyhult
57c26c13d9
Redo cases for simplification
2021-04-12 19:21:58 +02:00
Phil Ewels
2f77d16b70
Merge pull request #220 from ewels/master
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UPPMAX: Avoid undefined parameter warnings
2021-04-08 15:06:00 +02:00
Pontus Freyhult
be6ea0060f
Wrap sinfo call in a try/catch and default to rackham on failure
2021-04-08 09:49:42 +02:00
Pontus Freyhult
fa1b4cb412
Move cluster options creating closure out of process scope
2021-04-08 09:45:29 +02:00
James A. Fellows Yates
161c3a33d4
Merge branch 'master' into eva
2021-04-07 19:28:16 +02:00
James A. Fellows Yates
ce465cca57
Apply suggestions from code review
...
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
2021-04-07 19:27:24 +02:00
Pontus Freyhult
4d64db85eb
Determine cluster through slurm
2021-04-07 18:43:32 +02:00
Pontus Freyhult
c5070f3eba
Use node queue when more memory than thin nodes have
2021-04-07 18:43:32 +02:00
Alexander Peltzer
91f50aad4e
Merge pull request #221 from phue/biohpc_gen
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Add BioHPC Genomics config
2021-04-07 14:03:22 +02:00
ameynert
0ab9edde72
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
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
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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
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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
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Added JAX conf
2021-03-24 03:31:14 -04:00
Alexander Peltzer
5988c51361
Merge pull request #211 from DoaneAS/master
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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
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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
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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
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Modified ampliseq-specific uppmax-config
2020-12-02 13:40:43 +01:00