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Author SHA1 Message Date
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
87c8e346e0
fix(sysbio): Change filetype 2021-06-17 08:14:48 -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
7ff1c6cc7d
ci: Add sysbio 2021-06-16 21:19:49 -05:00
Edmund Miller
2a958f5ce3
docs: Add sysbio 2021-06-16 21:19:38 -05:00
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
Gisela Gabernet
9cca0eaf85
Merge pull request #250 from ggabernet/master 
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 
Update cfc.config
 2021-06-11 14:42:37 +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
Maxime U. Garcia
483e24aab6
Merge pull request #242 from maxulysse/master_munin 
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
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
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 
Add Cambridge University HPC config
 2021-04-25 10:40:56 +02:00
Alexander Peltzer
d624313abd
Merge pull request #236 from aunderwo/sanger 
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