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
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
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
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
Asaf Peer
a0c8a9ec8f
updated jax resources
2021-04-12 16:00:34 -04:00
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
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
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
