Gisela Gabernet
e2088a008d
Merge branch 'master' into master
2021-07-03 12:24:42 +02:00
ggabernet
f8690d49e8
add to tests
2021-07-03 12:21:03 +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
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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
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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
9298b353f5
Merge pull request #253 from jfy133/eva
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eager@EVA fixes more SGE + java silliness
2021-06-29 12:53:34 +02:00
James A. Fellows Yates
5f4b915ae8
Update eva.config
2021-06-29 11:31:00 +02:00
ameynert
85c3f07f3c
Merge pull request #3 from nf-core/master
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Merge in from nf-core/configs
2021-06-25 10:39:18 +01:00
Harshil Patel
93cfc48afd
Add ARTIC v4 primers to genomes config
2021-06-21 21:04:16 +01:00
Edmund Miller
3019035fdb
Merge pull request #252 from Emiller88/utd_sysbio
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Add UTD sysbio
2021-06-17 14:36:30 +00:00
Edmund Miller
cb213a499c
ci: Another missing comma
2021-06-17 09:34:03 -05:00
Edmund Miller
5ad959a436
fix(sysbio): Missing comma
2021-06-17 09:18:45 -05:00
Edmund Miller
f9e4ec4a8d
fix(sysbio): Add sysbio to rnaseq
2021-06-17 09:18:45 -05:00
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
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
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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
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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
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
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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
Barry digby
24a4119e43
memory test
2021-04-29 14:24:57 +01:00
