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
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
Gisela Gabernet
9cca0eaf85
Merge pull request #250 from ggabernet/master
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cfc config
2021-06-11 15:05:16 +02:00
ggabernet
c3385593cb
revert cfc config
2021-06-11 14:59:09 +02:00
Gisela Gabernet
1f45b9c297
Merge pull request #249 from nf-core/mseybold-patch-1
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Update cfc.config
2021-06-11 14:42:37 +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
Maxime U. Garcia
483e24aab6
Merge pull request #242 from maxulysse/master_munin
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feat: update owner of munin profile
2021-05-20 10:08:32 +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
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
Phil Ewels
fb40b27eab
Merge pull request #237 from maxulysse/master_opengraph
2021-04-26 17:23:08 +02:00
MaxUlysse
867e1aff61
feat: remove social preview image to use GitHub OpenGraph
2021-04-26 12:41:56 +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
Alexander Peltzer
d624313abd
Merge pull request #236 from aunderwo/sanger
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Add Sanger to README
2021-04-25 10:40:41 +02:00
Anthony Underwood
e1b1402f50
Add Cambridge to README
2021-04-24 13:22:54 +01:00
Anthony Underwood
5aadc5ec0e
Add Sanger to README
2021-04-24 13:21:19 +01:00
FriederikeHanssen
9cf19d5246
Merge pull request #210 from FriederikeHanssen/cfc_sarek
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Cfc sarek
2021-04-23 17:22:01 +02:00
Gisela Gabernet
4e9e5d2c67
Merge branch 'master' into cfc_sarek
2021-04-23 16:47:04 +02:00
Anthony Underwood
b660cb7c09
Merge pull request #234 from aunderwo/sanger
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Add a Sanger config and documentation
2021-04-22 16:41:33 +01:00
Anthony Underwood
982d1a8f2a
Fix markdown linting
2021-04-22 16:41:05 +01:00
Anthony Underwood
29dcc160e3
Create cambridge.md
2021-04-22 16:04:29 +01:00
Anthony Underwood
8b3951b244
Create cambridge.config
2021-04-22 16:00:37 +01:00
Anthony Underwood
3e8f9b3d4e
Remove blank lines
2021-04-22 15:57:09 +01:00
Anthony Underwood
f414446a88
Add info on how to load Singularity into your path
2021-04-22 15:38:36 +01:00
Anthony Underwood
b16b011bcc
Add ~/bin as recommended location for nextflow executable
2021-04-22 12:02:11 +01:00
Anthony Underwood
351c5773f0
Add queue limits for 'normal'
2021-04-22 11:59:34 +01:00
Anthony Underwood
fa267c0cf9
Add sanger to tests
2021-04-21 21:01:25 +01:00
Anthony Underwood
6175362049
Add sanger profile
2021-04-21 20:47:48 +01:00
Anthony Underwood
cc18d213dc
Update sanger.md
2021-04-21 20:24:08 +01:00
Anthony Underwood
40eb3e0201
Update sanger.md
2021-04-21 20:20:30 +01:00
Anthony Underwood
7163e8723d
Create sanger.md
2021-04-21 20:17:42 +01:00
Anthony Underwood
7d8770af1a
Create sanger.config
2021-04-21 16:39:55 +01:00
Maxime Garcia
7498e29ec0
Merge pull request #201 from maxulysse/master_uppmax_offline
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Improve offline docs for Bianca
2021-04-21 13:04:15 +02:00
Maxime Garcia
1548690ca6
Update docs/uppmax.md
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Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
2021-04-21 12:27:27 +02:00
Patrick Hüther
fff04ce0ba
Merge pull request #233 from phue/biohpc_gen
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biohpc_gen: update software tree path
2021-04-21 12:14:06 +02:00
MaxUlysse
bab9241243
fix: markdownlint
2021-04-21 11:51:14 +02:00
