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Author SHA1 Message Date
Barry digby
04c0da5a2f nuig confg (lugh) 2021-07-27 17:05:27 +01:00
MaxUlysse
895c4eb610 fix: closes #260 + sort some lines 2021-07-27 16:35:19 +02:00
Harshil Patel
6ede44b221
Merge pull request #258 from ameynert/master 
Update eddie config docs & added viralrecon config
 2021-07-22 15:14:54 +01:00
ameynert
2112168420
Set BLASTDB_LMDB_MAP_SIZE 
This environment variable needs to be set in order to prevent memory allocation errors in the MAKEBLASTDB process.
 2021-07-22 15:07:19 +01:00
ameynert
17fad9dd15
Update pipeline/viralrecon.config 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-21 12:27:09 +01:00
ameynert
d9abb7d59f
Added eddie config to viralrecon 2021-07-21 12:23:47 +01:00
ameynert
5224eb5574
Updated resources folder & institute name 
Local resources folder was re-organized & re-named BioinformaticsResources. Added note about viralrecon & atacseq pipeline-specific config. IGMM name-changed recently; updated to IGC.
 2021-07-21 12:15:17 +01:00
ameynert
4ceb369af5
eddie.config for viralrecon pipeline 2021-07-21 12:10:43 +01:00
ameynert
0da2c57784
Merge pull request #4 from nf-core/master 
Merge from nf-core/configs
 2021-07-21 12:09:32 +01:00
Maxime U. Garcia
47217cae5b
Merge pull request #231 from maxulysse/master_kraken 
Remove kraken profile
 2021-07-20 09:29:47 +02:00
Maxime U. Garcia
30e058abf0
Merge branch 'master' into master_kraken 2021-07-20 09:26:56 +02:00
Harshil Patel
836d3c4015
Merge pull request #257 from drpatelh/V1200 
Add ARTIC v1200 primers to genomes config for viralrecon
 2021-07-12 14:03:29 +01:00
Harshil Patel
962dca7a46 Add ARTIC v1200 primers to genomes config for viralrecon 2021-07-12 12:24:49 +01:00
Gisela Gabernet
435955ab20
Merge pull request #256 from ggabernet/master 
Add AWS tower config
 2021-07-03 16:54:59 +02:00
ggabernet
e6f1bfaa1a finally add profile 2021-07-03 15:13:10 +02:00
ggabernet
68e12f85ec fix cchecker 2021-07-03 15:11:51 +02:00
ggabernet
2a69b90be6 fix cchecker 2021-07-03 15:09:43 +02:00
ggabernet
6475671c38 test that it fails 2021-07-03 14:57:58 +02:00
ggabernet
926f3ba24f update checker script 2021-07-03 14:52:44 +02:00
ggabernet
79fffbd77f update changes 2021-07-03 14:39:17 +02:00
ggabernet
f3274c49b5 test profile multiline 2021-07-03 14:36:56 +02:00
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 
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 
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 
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 
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 
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 
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