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581 commits

Author SHA1 Message Date
James A. Fellows Yates
c799784629
Merge pull request #273 from jfy133/mpcdf-fix 
Add auto-cleanup for MPCDF
 2021-09-09 13:41:29 +02:00
Theo Portlock
05ad3e0577
Update conf/rosalind.config 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2021-09-09 13:37:02 +02:00
James A. Fellows Yates
d479926c7f
Update mpcdf.config 2021-09-09 13:33:56 +02:00
James A. Fellows Yates
7ec12b6736
Update eva.config 2021-09-09 13:10:05 +02:00
James A. Fellows Yates
96e26a5411
Merge pull request #272 from jfy133/eva-eager-subprofiles 
Bump additional library merge memory for eager @ EVA
 2021-09-08 15:25:07 +02:00
James A. Fellows Yates
4286a3a342
Bump additional library merge memor 2021-09-08 15:16:40 +02:00
theoportlock
b240142cc3 Adds rosalind configuration 2021-09-08 14:33:39 +02:00
Rogan Grant
a7aca37bc8
Set autoMounts to true 2021-09-06 15:15:46 -05:00
Rogan Grant
b56b7b310b
Merge pull request #266 from RoganGrant/master 
Northwestern University Genomics Nodes (new add)
 2021-09-06 13:26:49 -05:00
James A. Fellows Yates
39f54db097
Update container cache 2021-09-05 12:09:02 +02:00
James A. Fellows Yates
59a0901b68
Add library merge steps to have overhead 2021-09-05 12:07:53 +02:00
Rogan Grant
54298ca0f7
Merge branch 'nf-core:master' into master 2021-09-04 15:37:03 -05:00
rogangrant
a8d06ee356 Revert "Forgot a slash :(" 
This reverts commit d5601fea84.
 2021-09-04 15:36:05 -05:00
Rogan Grant
d5601fea84 Forgot a slash :( 2021-09-04 15:19:32 -05:00
Rogan Grant
2c5e454d16 Updated iGenomes path for odd local structure on Quest 2021-09-04 15:13:41 -05:00
Marc Trunjer Kusk Nielsen
1bf2d436d4
Update computerome.config 2021-09-01 22:21:31 +02:00
Marc Trunjer Kusk Nielsen
e2d54cb56c
Update computerome.config 2021-09-01 22:06:56 +02:00
Marc Trunjer Kusk Nielsen
a1413ce18e
Update computerome.config 2021-09-01 21:47:48 +02:00
Marc Trunjer Kusk Nielsen
d4c71f0d8d
Update computerome.config 2021-09-01 13:22:31 +02:00
Marc Trunjer Kusk Nielsen
fdac67afbf
Create computerome.config 2021-08-31 13:58:39 +02:00
James A. Fellows Yates
94cbb031c6
Update eva.config 2021-08-30 13:29:44 +02:00
Patrick Hüther
6c4998fa8a
reduce max_memory to 1.8TB 2021-08-27 14:01:34 +02:00
James A. Fellows Yates
5fbd938bc1
Export user env too 2021-08-27 10:08:20 +02:00
James A. Fellows Yates
bcb844f896
Merge pull request #268 from jfy133/master 
Delete SHH profiles due to decommissioning
 2021-08-23 14:08:13 +02:00
James Fellows Yates
59af7f0eee Delete SHH profiles due to decommissioning 2021-08-20 10:15:39 +02:00
James A. Fellows Yates
6701354060
Add genotyping_ug to SGE fixes 2021-08-20 10:11:11 +02:00
James Fellows Yates
b0e344846d Changes after code review from @aidaanva 2021-08-04 10:37:49 +02:00
James Fellows Yates
76fc461670 Try new strategy for SGE/JAVA bs 2021-08-04 10:14:56 +02:00
Rogan Grant
f793ffaace Updated iGenomes location 2021-08-03 15:10:54 -05:00
James A. Fellows Yates
00491de038
Update eva.config 2021-08-03 13:54:14 +02:00
Rogan Grant
24a2949fe2 Had executor options in wrong spot :( 2021-07-28 18:05:45 -05:00
Rogan Grant
6862fb8bfd testing ternary operatory 2021-07-28 18:01:03 -05:00
Rogan Grant
bcc69fe83c Enable use of himem nodes 2021-07-28 17:54:51 -05:00
Rogan Grant
ac11ca5568 Remove echo used for testing 2021-07-28 16:48:08 -05:00
Rogan Grant
3dd4f16d09 Added indicator for testing 2021-07-28 14:01:12 -05:00
Rogan Grant
09ed4d54b9 Just make command a single line for simplicity 2021-07-28 13:52:26 -05:00
Rogan Grant
09e0ea2674 typo 2021-07-28 13:46:40 -05:00
Rogan Grant
e1e0810d1b Clean up module loading script 2021-07-28 13:44:48 -05:00
Rogan Grant
e2c566ed13 Testing "automounts" 2021-07-28 13:38:06 -05:00
Rogan Grant
f104250ff4 Removed comment 2021-07-28 13:34:49 -05:00
Rogan Grant
9df267a192 Merged duplicate params 2021-07-28 13:27:17 -05:00
Rogan Grant
ff6823ec1d removed unnecessary space 2021-07-28 13:22:52 -05:00
Rogan Grant
9957e9eea1 Version 1 of custom config with queue-switching for long jobs and module loading 2021-07-28 13:11:02 -05:00
Barry digby
70b2644c9a . 2021-07-27 17:39:37 +01:00
Barry digby
2b6e80561a Merge branch 'master' of https://github.com/nf-core/configs into 2021-07-27 17:13:17 +01:00
Barry digby
4f962260d0 s 2021-07-27 17:08:53 +01:00
Barry digby
04c0da5a2f nuig confg (lugh) 2021-07-27 17:05:27 +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
4ceb369af5
eddie.config for viralrecon pipeline 2021-07-21 12:10:43 +01:00
Maxime U. Garcia
30e058abf0
Merge branch 'master' into master_kraken 2021-07-20 09:26:56 +02:00
Harshil Patel
962dca7a46 Add ARTIC v1200 primers to genomes config for viralrecon 2021-07-12 12:24:49 +01:00
Gisela Gabernet
e2088a008d
Merge branch 'master' into master 2021-07-03 12:24:42 +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
5f4b915ae8
Update eva.config 2021-06-29 11:31:00 +02:00
Harshil Patel
93cfc48afd Add ARTIC v4 primers to genomes config 2021-06-21 21:04:16 +01:00
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
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
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
ggabernet
c3385593cb revert cfc config 2021-06-11 14:59:09 +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
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 
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
Alexander Peltzer
c12c373969
Merge pull request #235 from aunderwo/cambridge 
Add Cambridge University HPC config
 2021-04-25 10:40:56 +02:00
Gisela Gabernet
4e9e5d2c67
Merge branch 'master' into cfc_sarek 2021-04-23 16:47:04 +02:00
Anthony Underwood
8b3951b244
Create cambridge.config 2021-04-22 16:00:37 +01:00
Anthony Underwood
351c5773f0
Add queue limits for 'normal' 2021-04-22 11:59:34 +01:00
Anthony Underwood
7d8770af1a
Create sanger.config 2021-04-21 16:39:55 +01:00
phue
b225a0555a biohpc_gen: update software tree path 2021-04-21 10:08:00 +02:00
James A. Fellows Yates
eacdf89e53
Update eva.config 2021-04-20 13:17:35 +02:00
James A. Fellows Yates
b9a00f7926
Update mpcdf.config 2021-04-15 22:27:07 +02:00
Harshil Patel
7ac66dcd72
Update crick.config 2021-04-13 17:07:02 +01:00
Combiz Khozoie
c571c05ab9
Merge pull request #219 from slacalle/patch-2 
Imperial College | Remove "/rdsgpfs"
 2021-04-13 15:28:00 +01:00