ameynert
5224eb5574
Updated resources folder & institute name
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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
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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
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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
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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
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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
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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
