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632 commits

Author SHA1 Message Date
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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