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
...
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
...
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
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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
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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
Alexander Peltzer
99985c658f
Merge pull request #194 from marcel-keller/ebc
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Update ebc.config
2020-11-26 14:12:33 +01:00
marcel-keller
5590a9743a
Update ebc.config
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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
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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
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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
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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
2020-09-13 20:46:14 -05:00
Edmund Miller
dc2735207e
feat(utd): add Kim queue
2020-09-13 20:46:10 -05:00
James A. Fellows Yates
3b7902d11b
Mad multi-core increase CPUs on retry
2020-09-06 08:23:35 +02:00
James A. Fellows Yates
4335e5deb7
Update mpcdf.config
2020-09-04 20:17:09 +02:00
James A. Fellows Yates
b4e275c3b9
Add MPCDF for EAGER
2020-09-04 19:57:25 +02:00
James A. Fellows Yates
5c7ab234b6
Create mpcdf.config
2020-09-04 19:55:40 +02:00
James A. Fellows Yates
0a685c1cc2
Update mpcdf.config
2020-09-03 20:24:11 +02:00
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
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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
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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