FriederikeHanssen
f1756ba121
Merge branch 'nf-core:master' into cfc
2021-10-04 18:04:18 +02:00
pierrespc
1621585558
improving documentation
2021-10-04 16:08:33 +02:00
pierrespc
e5d4a357c5
clean doc
2021-10-04 15:08:01 +02:00
Falko Hofmann
0950eb3518
Merge pull request #251 from phue/cbe_singularity_workaround
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cbe: send SIGUSR2 upon job termination
2021-10-04 13:24:53 +02:00
Rike
f6e16f2872
Add check_resource to respect max_resource/max_cpus
2021-10-04 10:14:02 +02:00
pierrespc
f6266879d6
edited maestronuclear and maestromitocondrial configs. The latter has not been optimized yet
2021-09-29 13:47:35 +02:00
pierrespc
b71df6fe57
renamed eager pipeline config file
2021-09-29 13:22:07 +02:00
pierrespc
9ea3e2096a
long and normal qos profiles defined now in an unique maestro config file. maestro.config also defined in pipeline/eager for ressources assignation to specific processes
2021-09-29 13:11:14 +02:00
Bjørn Peare Bartholdy
e750a6d445
Update conf/alice.config
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-09-28 13:34:12 +02:00
Bjørn Peare Bartholdy
197bd6cfb1
Merge branch 'nf-core:master' into master
2021-09-28 12:09:50 +02:00
bbartholdy
b6ccb46383
add ALICE profile
2021-09-28 12:08:27 +02:00
Mei Wu
79a79f7d8d
added pipeline-specific config
2021-09-28 10:38:25 +02:00
Mei Wu
c2d74b290a
fix md
2021-09-27 16:25:02 +02:00
Mei Wu
a8a2027f70
Merge branch 'master' into hasta
2021-09-27 16:12:23 +02:00
Mei Wu
06fac1dcfc
initial commit
2021-09-27 16:05:32 +02:00
Mei Wu
ae0adb056f
initial commit
2021-09-27 16:05:19 +02:00
Anthony Underwood
7469e20b4e
change max_time diretcive in the correct place
2021-09-25 09:23:24 +01:00
Anthony Underwood
6a970dc4a8
update max time for long queue
2021-09-23 11:59:45 +01:00
Patrick Hüther
1cbe2759c4
fix invalid rapid qos selection
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it only applies to the c partition
2021-09-22 11:54:27 +02:00
pierrespc
3e22b85b02
maestro only for normal qos
2021-09-22 10:13:46 +02:00
Anthony Underwood
50df2105fb
update long jobs to be submitted to the long queue
2021-09-21 14:42:59 +01:00
pierrespc
3b593d46ec
merged two pasteur config files for maestro
2021-09-20 15:14:50 +02:00
Harshil Patel
5068e4806f
Merge pull request #271 from theoportlock/master
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Adds Rosalind config for KCL!
2021-09-17 13:36:19 +01:00
Harshil Patel
3b95fd9ee3
Update conf/rosalind.config
2021-09-17 13:15:09 +01:00
theoportlock
9116a09afe
Fixes formatting and ignore_params
2021-09-17 13:21:32 +02:00
pierrespc
4614ff6f45
change max mem in Normal
2021-09-16 16:50:45 +02:00
pierrespc
de2a745fde
change type in Normal name
2021-09-16 16:48:26 +02:00
pierrespc
482e7cf8de
2 config files for Maestro HPC at Pasteur Institute, Paris
2021-09-16 12:40:56 +02:00
Marc Trunjer Kusk Nielsen
a55c3c04eb
Update computerome.config
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Adding genomes and modules back into schema_ingore_params to avoid warnings about unexpected parameters.
2021-09-15 19:54:51 +02:00
Marc Trunjer Kusk Nielsen
8b29b5584e
Update computerome.config
2021-09-15 14:20:02 +02:00
Marc Trunjer Kusk Nielsen
ab8a9ad0b8
Update computerome.config
2021-09-15 13:27:23 +02:00
theoportlock
9c97220919
Merge branch 'master' of https://github.com/theoportlock/configs
2021-09-15 11:43:09 +02:00
theoportlock
3c86f8f47c
Removes the broken clusterOptions
2021-09-15 11:42:43 +02:00
Marc Trunjer Kusk Nielsen
aad70fe86d
Merge branch 'nf-core:master' into computerome
2021-09-15 11:08:48 +02:00
Marc Trunjer Kusk Nielsen
29003e13f1
Update computerome.config
2021-09-15 10:22:57 +02:00
James A. Fellows Yates
a7b1183065
Remove 1CPU for host removal fastq
2021-09-14 11:52:21 +02:00
Marc Trunjer Kusk Nielsen
86e21b378a
Update computerome.config
2021-09-13 14:26:10 +02:00
Marc Trunjer Kusk Nielsen
275288632d
Update computerome.config
2021-09-13 14:22:22 +02:00
Marc Trunjer Kusk Nielsen
366f945a40
Update computerome.config
2021-09-13 14:20:55 +02:00
Marc Trunjer Kusk Nielsen
8ebdd43898
Update computerome.config
2021-09-13 14:01:35 +02:00
Marc Trunjer Kusk Nielsen
1071eb9d2e
Update computerome.config
2021-09-13 13:38:46 +02:00
Marc Trunjer Kusk Nielsen
2e515dc861
Update computerome.config
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Don't raise an error when --project is specified
2021-09-13 13:38:25 +02:00
Marc Trunjer Kusk Nielsen
e5cba18c9b
Update computerome.config
2021-09-13 13:28:33 +02:00
Marc Trunjer Kusk Nielsen
0327ef40ea
Update computerome.config
2021-09-13 13:20:57 +02:00
Marc Trunjer Kusk Nielsen
a0ba05fd99
Update computerome.config
2021-09-13 08:36:30 +02:00
Marc Trunjer Kusk Nielsen
84f94d92c4
Update computerome.config
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Added a way to use `--project` to provide project information to the scheduler. Inspired by the uppmax config
2021-09-10 15:10:19 +02:00
Marc Trunjer Kusk Nielsen
463df26c72
Merge branch 'nf-core:master' into computerome
2021-09-10 14:47:05 +02:00
James A. Fellows Yates
7c639ac934
Bump lib merge further
2021-09-09 14:47:20 +02:00
James A. Fellows Yates
0603aba342
Remove debugging stuff
2021-09-09 13:54:01 +02:00
James A. Fellows Yates
c799784629
Merge pull request #273 from jfy133/mpcdf-fix
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Add auto-cleanup for MPCDF
2021-09-09 13:41:29 +02:00
Theo Portlock
05ad3e0577
Update conf/rosalind.config
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-09 13:37:02 +02:00
James A. Fellows Yates
d479926c7f
Update mpcdf.config
2021-09-09 13:33:56 +02:00
James A. Fellows Yates
7ec12b6736
Update eva.config
2021-09-09 13:10:05 +02:00
James A. Fellows Yates
96e26a5411
Merge pull request #272 from jfy133/eva-eager-subprofiles
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Bump additional library merge memory for eager @ EVA
2021-09-08 15:25:07 +02:00
James A. Fellows Yates
4286a3a342
Bump additional library merge memor
2021-09-08 15:16:40 +02:00
theoportlock
b240142cc3
Adds rosalind configuration
2021-09-08 14:33:39 +02:00
Rogan Grant
a7aca37bc8
Set autoMounts to true
2021-09-06 15:15:46 -05:00
Rogan Grant
b56b7b310b
Merge pull request #266 from RoganGrant/master
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Northwestern University Genomics Nodes (new add)
2021-09-06 13:26:49 -05:00
James A. Fellows Yates
39f54db097
Update container cache
2021-09-05 12:09:02 +02:00
James A. Fellows Yates
59a0901b68
Add library merge steps to have overhead
2021-09-05 12:07:53 +02:00
Rogan Grant
54298ca0f7
Merge branch 'nf-core:master' into master
2021-09-04 15:37:03 -05:00
rogangrant
a8d06ee356
Revert "Forgot a slash :("
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This reverts commit d5601fea84
.
2021-09-04 15:36:05 -05:00
Rogan Grant
d5601fea84
Forgot a slash :(
2021-09-04 15:19:32 -05:00
Rogan Grant
2c5e454d16
Updated iGenomes path for odd local structure on Quest
2021-09-04 15:13:41 -05:00
Marc Trunjer Kusk Nielsen
1bf2d436d4
Update computerome.config
2021-09-01 22:21:31 +02:00
Marc Trunjer Kusk Nielsen
e2d54cb56c
Update computerome.config
2021-09-01 22:06:56 +02:00
Marc Trunjer Kusk Nielsen
a1413ce18e
Update computerome.config
2021-09-01 21:47:48 +02:00
Marc Trunjer Kusk Nielsen
d4c71f0d8d
Update computerome.config
2021-09-01 13:22:31 +02:00
Marc Trunjer Kusk Nielsen
fdac67afbf
Create computerome.config
2021-08-31 13:58:39 +02:00
James A. Fellows Yates
94cbb031c6
Update eva.config
2021-08-30 13:29:44 +02:00
Patrick Hüther
6c4998fa8a
reduce max_memory to 1.8TB
2021-08-27 14:01:34 +02:00
James A. Fellows Yates
5fbd938bc1
Export user env too
2021-08-27 10:08:20 +02:00
James A. Fellows Yates
bcb844f896
Merge pull request #268 from jfy133/master
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Delete SHH profiles due to decommissioning
2021-08-23 14:08:13 +02:00
James Fellows Yates
59af7f0eee
Delete SHH profiles due to decommissioning
2021-08-20 10:15:39 +02:00
James A. Fellows Yates
6701354060
Add genotyping_ug to SGE fixes
2021-08-20 10:11:11 +02:00
James Fellows Yates
b0e344846d
Changes after code review from @aidaanva
2021-08-04 10:37:49 +02:00
James Fellows Yates
76fc461670
Try new strategy for SGE/JAVA bs
2021-08-04 10:14:56 +02:00
Rogan Grant
f793ffaace
Updated iGenomes location
2021-08-03 15:10:54 -05:00
James A. Fellows Yates
00491de038
Update eva.config
2021-08-03 13:54:14 +02:00
Rogan Grant
24a2949fe2
Had executor options in wrong spot :(
2021-07-28 18:05:45 -05:00
Rogan Grant
6862fb8bfd
testing ternary operatory
2021-07-28 18:01:03 -05:00
Rogan Grant
bcc69fe83c
Enable use of himem nodes
2021-07-28 17:54:51 -05:00
Rogan Grant
ac11ca5568
Remove echo used for testing
2021-07-28 16:48:08 -05:00
Rogan Grant
3dd4f16d09
Added indicator for testing
2021-07-28 14:01:12 -05:00
Rogan Grant
09ed4d54b9
Just make command a single line for simplicity
2021-07-28 13:52:26 -05:00
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
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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
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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
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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
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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
ikeller
ae114dd142
edit max_time
2021-05-20 13:52:13 +02:00
ikeller
5a0ecbd81d
edit max_time
2021-05-20 13:48:59 +02:00
ikeller
6def686ab5
edit config
2021-05-20 13:44:59 +02:00
ikeller
0e3898eabf
modify singularity settings
2021-05-20 10:53:35 +02:00
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
Asaf Peer
82fadc7061
replaced owner in JAX
2021-05-19 13:48:49 -04:00
Phil Ewels
9c4830c8d5
Merge pull request #238 from nf-core/hebbe-config-fix
2021-05-19 17:46:52 +02:00
ikeller
af1e57027d
edit config and readme
2021-05-19 09:46:07 +02:00
ikeller
fb3cede5d3
add config file
2021-05-19 08:41:55 +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
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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
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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
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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
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Java processes with overhead memory requirements
2021-03-30 16:31:00 +01:00
ameynert
e5f2a63079
Java overhead processes list updated
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Added all processes calling GATK for Mutect2 variant calling
2021-03-30 16:21:53 +01:00
ameynert
adfb5366b9
Java overhead process list updated
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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"
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"/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
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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
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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
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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