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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
..
pipeline Merge pull request #248 from jfy133/eva 2021-06-07 13:26:05 +02:00
abims.config Add ABiMS - autoMounts = false 2020-10-22 18:18:55 +02:00
awsbatch.config update aws clipath 2021-02-09 22:06:59 +01:00
bi.config reduce complexity 2020-07-07 13:48:28 +02:00
bigpurple.config added nyu prince and bigpurple md files, added singularity cacheDir to prince and bigpurple configs 2019-04-18 14:13:02 -04:00
binac.config Update binac.config 2020-02-19 11:27:02 +01:00
biohpc_gen.config biohpc_gen: update software tree path 2021-04-21 10:08:00 +02:00
cambridge.config Create cambridge.config 2021-04-22 16:00:37 +01:00
cbe.config cbe: send SIGUSR2 upon job termination 2021-06-16 16:36:39 +02:00
ccga_dx.config Updating the CCGA DX profile to new storage system 2021-02-16 09:02:16 +01:00
ccga_med.config Adding new CCGA Med Cluster to profiles 2020-02-11 11:12:51 +01:00
cfc.config revert cfc config 2021-06-11 14:59:09 +02:00
cfc_dev.config Add scratch = true to avoid writing of intermediate file to /tmp 2020-05-04 17:09:43 +02:00
crick.config Update crick.config 2021-04-13 17:07:02 +01:00
czbiohub_aws.config executor.cli --> aws.batch.cliPath 2021-05-19 13:36:15 -07:00
denbi_qbic.config Mini adjustment for highmem queue on denbi 2019-11-27 14:23:01 +01:00
ebc.config change of directory for conda environments 2020-12-09 15:11:21 +02:00
eddie.config Add TMPDIR and mount for it to singularity configuration 2021-05-25 09:54:08 +01:00
eva.config Apply suggestions from code review 2021-04-07 19:27:24 +02:00
genotoul.config Add genotoul fix 2019-11-26 16:09:08 +01:00
genouest.config deprecate igenomesIgnore in favor of igenomes_ignore 2019-10-28 11:38:24 +01:00
gis.config Removed params.config_profile_name, added params.hostnames 2019-03-13 17:19:34 +01:00
google.config First commit of Google Cloud config 2020-03-06 05:47:29 +00:00
hebbe.config Fix hebbe withName regex 2021-04-29 23:06:56 +02:00
icr_davros.config reverting autoMounts due to bug 2020-06-26 13:39:37 +01:00
ifb_core.config Add IFB config 2021-03-16 15:54:19 +01:00
imperial.config Remove "/rdsgpfs" 2021-03-25 12:38:15 +00:00
imperial_mb.config fixed indents 2020-12-18 15:34:56 +00:00
jax.config updated jax resources 2021-04-12 16:00:34 -04:00
kraken.config Added kraken config (#15) 2019-08-05 11:19:05 +02:00
mpcdf.config Update mpcdf.config 2021-04-15 22:27:07 +02:00
munin.config fix: forgotten } 2021-05-20 09:37:48 +02:00
oist.config Institutional profile for Okinawa Institute of Science and Technology 2021-02-02 17:40:10 +09:00
pasteur.config deprecate igenomesIgnore in favor of igenomes_ignore 2019-10-28 11:38:24 +01:00
phoenix.config Removed params.config_profile_name, added params.hostnames 2019-03-13 17:19:34 +01:00
prince.config Nice prince 2019-11-26 14:29:52 +01:00
sanger.config Add queue limits for 'normal' 2021-04-22 11:59:34 +01:00
seg_globe.config Remove ceh profile for now 2021-01-21 13:15:08 +01:00
shh.config update shh config after CDAG departure 2021-02-17 10:22:05 +01:00
uct_hpc.config Copy over HPC config 2020-06-17 15:20:22 +02:00
uppmax.config UPPMAX: add to schema_ignore_params 2021-03-26 15:22:57 +01:00
utd_ganymede.config fix(ganymede): large => high 2021-03-22 12:42:56 -05:00
uzh.config Removed params.config_profile_name, added params.hostnames 2019-03-13 17:19:34 +01:00
wcm.config Create wcm.config 2021-03-11 13:52:11 -05:00