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Author SHA1 Message Date
Marc Trunjer Kusk Nielsen
463df26c72
Merge branch 'nf-core:master' into computerome 2021-09-10 14:47:05 +02:00
James A. Fellows Yates
7c639ac934 Bump lib merge further 2021-09-09 14:47:20 +02:00
James A. Fellows Yates
0603aba342
Remove debugging stuff 2021-09-09 13:54:01 +02:00
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
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
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
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
MaxUlysse
3918e0aa9d feat: remove kraken profile 2021-04-13 15:14:14 +02:00
Asaf Peer
a0c8a9ec8f updated jax resources 2021-04-12 16:00:34 -04:00
Pontus Freyhult
ff20f121f9 Support use of very fat node in snowy 2021-04-12 19:34:28 +02:00
Pontus Freyhult
0987cbe1be Better test for snowy 2021-04-12 19:32:21 +02:00
Pontus Freyhult
7be4279718 Handle different (unexpected) sinfo returns in different cases 2021-04-12 19:31:41 +02:00
Pontus Freyhult
57c26c13d9 Redo cases for simplification 2021-04-12 19:21:58 +02:00
Phil Ewels
2f77d16b70
Merge pull request #220 from ewels/master 
UPPMAX: Avoid undefined parameter warnings
 2021-04-08 15:06:00 +02:00
Pontus Freyhult
be6ea0060f Wrap sinfo call in a try/catch and default to rackham on failure 2021-04-08 09:49:42 +02:00
Pontus Freyhult
fa1b4cb412 Move cluster options creating closure out of process scope 2021-04-08 09:45:29 +02:00
James A. Fellows Yates
161c3a33d4
Merge branch 'master' into eva 2021-04-07 19:28:16 +02:00
James A. Fellows Yates
ce465cca57
Apply suggestions from code review 
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
 2021-04-07 19:27:24 +02:00
Pontus Freyhult
4d64db85eb Determine cluster through slurm 2021-04-07 18:43:32 +02:00
Pontus Freyhult
c5070f3eba Use node queue when more memory than thin nodes have 2021-04-07 18:43:32 +02:00
Alexander Peltzer
91f50aad4e
Merge pull request #221 from phue/biohpc_gen 
Add BioHPC Genomics config
 2021-04-07 14:03:22 +02:00
ameynert
0ab9edde72
Delete conf/pipeline/atacseq directory 
Pipeline-specific config not supported yet by ATAC-seq pipeline
 2021-04-07 09:24:30 +01:00
James A. Fellows Yates
832edaa450
Merge branch 'master' into eva 2021-04-06 17:51:46 +02:00
James Fellows Yates
be1d35840d Add EVA and EAGER@EVA 2021-04-06 17:48:16 +02:00
James Fellows Yates
d69af0f287 Merging 2021-04-06 16:42:22 +02:00
phue
60ae267e43 use SLURM_CLUSTERS env var 
this seems to be more reliable for queue checking than using the clusterOptions directive. See https://github.com/nextflow-io/nextflow/issues/807
 2021-04-06 11:35:01 +02:00
ameynert
6e201a71f4
ATAC-seq pipeline config 
Java processes with overhead memory requirements
 2021-03-30 16:31:00 +01:00
ameynert
e5f2a63079
Java overhead processes list updated 
Added all processes calling GATK for Mutect2 variant calling
 2021-03-30 16:21:53 +01:00
ameynert
adfb5366b9
Java overhead process list updated 
Added HaplotypeCaller and GenotypeGVCFs to set of processes that need Java overhead
 2021-03-30 16:15:17 +01:00
phue
8fc60e2e70 add config for biohpc_gen 2021-03-29 19:25:58 +02:00
Gisela Gabernet
71a97ba316
Merge pull request #185 from ggabernet/master 
awsbatch config update
 2021-03-28 20:59:40 +02:00
Phil Ewels
d34bc40841 UPPMAX: add to schema_ignore_params 2021-03-26 15:22:57 +01:00
Phil Ewels
eccc9ea8d5 Define params.project and params.clusterOptions in uppmax config 2021-03-26 15:20:32 +01:00
Santiago Lacalle
e2c583d558
Remove "/rdsgpfs" 
"/rdsgpfs" symlink will not be present on all nodes. Without that mount the container creation will fail.
 2021-03-25 12:38:15 +00:00
Alexander Peltzer
26b5904df1
Merge pull request #218 from asafpr/master 
added jax singularity cache dir
 2021-03-24 17:39:03 +01:00
Asaf Peer
922ab87eb0 added jax singularity cache dir 2021-03-24 11:25:47 -04:00
Phil Ewels
bfab371c94
Merge branch 'master' into master 2021-03-24 12:36:15 +01:00
ameyner2
da8cf2f207 Added pipeline-specific config files for rnaseq and sarek 2021-03-24 10:46:26 +00:00
Asaf Peer
9b2d5bfead
Merge pull request #216 from asafpr/master 
Added JAX conf
 2021-03-24 03:31:14 -04:00
Alexander Peltzer
5988c51361
Merge pull request #211 from DoaneAS/master 
Adding WCM.config for Weill Cornell Medicine cluster
 2021-03-23 14:58:27 +01:00
Edmund Miller
a6975cdd4e
fix(ganymede): large => high 
Co-authored-by: drpatelh <drpatelh@users.noreply.github.com>
 2021-03-22 12:42:56 -05:00
Edmund Miller
34ccce9531
fix(ganymede): Add process resources 
Trimgalore though it can be a bottom neck, doesn't require the 1 big
memory node we have and can be run on the genomics queue.
 2021-03-21 21:47:59 -05:00
Edmund Miller
4570718b12
fix(ganymede): Add TMPDIR and SINGULARITY_CACHEDIR env variables 2021-03-21 21:45:39 -05:00
Asaf Peer
30c864e112 added JAX conf 2021-03-21 06:49:11 -04:00
ameyner2
059d353a1e Removed Conda, added automount Singularity 2021-03-18 12:31:56 +00:00
Rike
6221b67bcf Give Strelka a complete compute node 2021-03-18 11:11:02 +01:00
Rike
b1846af9d3 reduce mapping resource further to compute node 2021-03-18 11:10:00 +01:00
FriederikeHanssen
67c93a4743
Update conf/pipeline/sarek/cfc.config 
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
 2021-03-18 11:06:38 +01:00
Rike
b70097e495 remove new line 2021-03-17 15:46:18 +01:00
ameyner2
d4cd07c646 Typo in beforescript 2021-03-17 09:21:26 +00:00
Noirot Céline
7e9f83ee81 Add IFB config 2021-03-16 15:54:19 +01:00
ameyner2
cfe13fe6c1 Fixed typo & added singularity tmpdir 2021-03-15 15:42:30 +00:00
Ashley S Doane
e7f8189dfc
Create wcm.config 2021-03-11 13:52:11 -05:00
Rike
bb124a9be8 Reduce vc to run on compute 2021-03-11 16:11:41 +01:00
FriederikeHanssen
79ddbe1fea Add missing bracket 2021-03-11 09:29:03 +01:00
FriederikeHanssen
0057132e02 remove check_reource statement 2021-03-11 09:27:08 +01:00
phue
da3bd2693d cbe: add rapid qos 
and update config url
 2021-03-10 11:26:01 +01:00
FriederikeHanssen
eb9012919c Set values for processes with max_mem/max_cpus 2021-03-10 11:16:18 +01:00
Graeme Grimes
babeccd020
changed # to // for comments 2021-03-04 16:45:21 +00:00
ameynert
6f09a233f0
Added singularity module 2021-03-04 14:46:23 +00:00
ameynert
3af2c6409f
Initial commit of eddie.config 2021-03-03 09:59:16 +00:00
maxibor
286e18b80c update shh config after CDAG departure 2021-02-17 10:22:05 +01:00
drpatelh
01a4f8559e Update links to be consistent 2021-02-16 13:17:16 +00:00
Harshil Patel
6ffaf922c5
Update genomes.config 2021-02-16 10:28:32 +00:00
Marc Hoeppner
1f2fce00aa Updating the CCGA DX profile to new storage system 2021-02-16 09:02:16 +01:00
Harshil Patel
4de0855218
Update genomes.config 2021-02-15 18:48:03 +00:00
drpatelh
9d500cf679 Reorder params 2021-02-15 17:02:26 +00:00
drpatelh
f283dfb2dc Add ARTIC primer sets to genome config 2021-02-15 16:58:30 +00:00
James Fellows Yates
537f52a640 Add MPI-EVA profile 2021-02-14 17:50:20 +01:00
ggabernet
9b5bcbd434 update aws clipath 2021-02-09 22:06:59 +01:00
ggabernet
0909708b97 update with upstream 2021-02-09 22:01:27 +01:00
James A. Fellows Yates
86566ddd3b
Merge pull request #204 from jfy133/master 
Add a 'big_data' profile for eager @ SHH
 2021-02-04 15:07:52 +01:00
James A. Fellows Yates
e32f1e46ff
Update shh.config 2021-02-04 08:13:16 +01:00
James A. Fellows Yates
c515a401c7
Update shh.config 2021-02-04 08:06:35 +01:00
James A. Fellows Yates
82fe8a04be
Update shh.config 2021-02-04 08:02:33 +01:00
James A. Fellows Yates
e7ac0bae13
Update shh.config 2021-02-04 08:00:57 +01:00
James A. Fellows Yates
eb725f9ea3
Update shh.config 2021-02-03 20:13:09 +01:00
Charles Plessy
1608b36dcf Institutional profile for Okinawa Institute of Science and Technology 2021-02-02 17:40:10 +09:00
Thiseas C. Lamnidis
713a032a36
Add debug profile 
which deactivates cleanup of workdir after successful run
 2021-01-26 15:08:21 +01:00
James A. Fellows Yates
26d164ca74
Remove ceh profile for now 2021-01-21 13:15:08 +01:00
Åshild J. Vågene
594985f1ee
Update and rename ceh.config to seg_globe.config 2021-01-21 11:43:34 +01:00
Åshild J. Vågene
8fa720b9cc
Update conf/ceh.config 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2021-01-21 11:15:06 +01:00
Åshild J. Vågene
f8973f153a
Update ceh.config 2021-01-21 00:31:49 +01:00
Åshild J. Vågene
91594dffea
Update ceh.config 2021-01-21 00:29:43 +01:00
Åshild J. Vågene
c11c26f15f
Create ceh.config 2021-01-20 23:45:26 +01:00
James A. Fellows Yates
1c25cb033b
Add big_data profile 2021-01-19 13:53:01 +01:00
rbpisupati
9b5ac5c89d added anaconda module for cbe 2021-01-15 12:55:46 +01:00
James A. Fellows Yates
a4c55b3ea9
Fix time limit 0-9 typo 2021-01-06 10:44:12 +01:00
Combiz Khozoie
17cf4e3b35 fixed indents 2020-12-18 15:34:56 +00:00
Combiz Khozoie
3824403b4e removed workDir from Imperial configs 2020-12-18 10:31:36 +00:00
Combiz Khozoie
a61992d144 Added institutional configs for Imperial and Imperial MEDBIO. Added institutional pipeline configs for scflow for Imperial and Imperial MEDBIO 2020-12-18 10:21:26 +00:00
marcel-keller
c9ceaff3b3
change of directory for conda environments 
change of directory due to recent changes in our infrastructure
 2020-12-09 15:11:21 +02:00
emnilsson
8cc2fc5ecb
Merge pull request #193 from emnilsson/master 
Modified ampliseq-specific uppmax-config
 2020-12-02 13:40:43 +01:00
Alexander Peltzer
99985c658f
Merge pull request #194 from marcel-keller/ebc 
Update ebc.config
 2020-11-26 14:12:33 +01:00
marcel-keller
5590a9743a
Update ebc.config 
queueSize to 64
 2020-11-26 15:05:25 +02:00
Emelie Nilsso
febf38dd8e Removed an old process so that only relevant processes are included 2020-11-26 13:38:47 +01:00
Emelie Nilsso
d61ed01d2d Updated process names according to ampliseq main.nf 2020-11-25 17:50:30 +01:00
Emelie Nilsso
37e7cfae2c Removed unnecessary code that was used to troubleshoot 2020-11-24 07:14:23 +01:00
Emelie Nilsso
cd59bba83e Merge branch 'master' of https://github.com/nf-core/configs 2020-11-24 07:10:05 +01:00
Emelie Nilsso
c47088cda2 Merge remote-tracking branch 'origin' 2020-11-23 21:34:08 +01:00
Emelie Nilsso
2ea06ffab8 Modified uppmax and ampliseq specific config to fit with the divided preparation of the database 2020-11-23 21:20:36 +01:00
Thiseas C. Lamnidis
71d1ff2226
Add params block to sdag queue 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2020-11-18 13:04:46 +01:00
Thiseas C. Lamnidis
da781907f2
Move sdag queue specification block in sdag profile 2020-11-17 19:45:06 +01:00
Maxime Borry
c95fd9d52f
Merge pull request #186 from jfy133/shh-singularity-runoptions 
Remove custom singularity runOptions from SHH config
 2020-11-10 15:39:40 +01:00
James A. Fellows Yates
9d4d682867
Update shh.config 2020-11-10 15:14:03 +01:00
Gisela Gabernet Garriga
885f0ce5f6 awsbatch config update 2020-11-09 22:41:38 +01:00
lecorguille
90d1f9072b Add ABiMS - autoMounts = false 2020-10-22 18:18:55 +02:00
lecorguille
a63ca751ee Add ABiMS 2020-10-22 16:57:41 +02:00
James A. Fellows Yates
804f53c58c
Merge pull request #178 from jfy133/master 
Add Max Planck Computing and Data Facility Cobra/Raven Clusters
 2020-10-22 13:34:11 +02:00
James A. Fellows Yates
3995057d7f
Update mpcdf.config 2020-10-22 10:42:46 +02:00
James A. Fellows Yates
05deeca2d6
Update mpcdf.config 2020-10-15 14:22:35 +02:00
James A. Fellows Yates
e26c22b2f1
Update shh.config 2020-09-29 14:03:35 +02:00
MaxUlysse
2ccbdd3367 update params to latest version 2020-09-28 13:59:42 +02:00
MaxUlysse
8c0cc4b9ec code polishing 2020-09-25 09:57:50 +02:00
MaxUlysse
81f910cc95 add specific BamQC config 2020-09-25 09:49:43 +02:00
MaxUlysse
fbe7bd133a update uppmax specific sarek config 2020-09-25 08:33:53 +02:00
James A. Fellows Yates
11f1fb71db
Update mpcdf.config 2020-09-16 10:21:58 +02:00
James A. Fellows Yates
bbbdd3cb0f
Update mpcdf.config 2020-09-16 10:21:42 +02:00
James A. Fellows Yates
5b3492d240
Update mpcdf.config 2020-09-16 10:21:26 +02:00
James A. Fellows Yates
3115963b3e
Update mpcdf.config 2020-09-15 19:53:27 +02:00
James A. Fellows Yates
c6f7573d01
Update mpcdf.config 2020-09-15 17:48:54 +02:00
James A. Fellows Yates
bf87ec24e7
Update mpcdf.config 2020-09-15 17:45:38 +02:00
Edmund Miller
2c06019d89
fix(utd): Add check for less than 12 cpu 2020-09-13 20:46:14 -05:00
Edmund Miller
dc2735207e
feat(utd): add Kim queue 2020-09-13 20:46:10 -05:00
James A. Fellows Yates
3b7902d11b
Mad multi-core increase CPUs on retry 2020-09-06 08:23:35 +02:00
James A. Fellows Yates
4335e5deb7
Update mpcdf.config 2020-09-04 20:17:09 +02:00
James A. Fellows Yates
b4e275c3b9
Add MPCDF for EAGER 2020-09-04 19:57:25 +02:00
James A. Fellows Yates
5c7ab234b6
Create mpcdf.config 2020-09-04 19:55:40 +02:00
James A. Fellows Yates
0a685c1cc2
Update mpcdf.config 2020-09-03 20:24:11 +02:00
James A. Fellows Yates
42a1a15970
Create mpcdf.config 2020-09-03 20:11:56 +02:00
James A. Fellows Yates
c3fa87e4bc
Add microbiome screening profile for NT sized MALT runs for nf-core/eager@SHH 2020-08-11 09:18:36 +02:00
drpatelh
b804076959 Remove hard Singularity version 2020-08-03 11:38:10 +01:00
maxibor
69a0bd572b add temporary CDAG setting for SHH config 2020-07-23 15:38:28 +02:00
James A. Fellows Yates
d38ffc289b
Merge pull request #173 from jfy133/shh-eager-hops-update 
Remove now deprecated EAGER flag for HOPS profile
 2020-07-20 11:34:49 +02:00
James A. Fellows Yates
57ac9257a9
Remove now deprecated EAGER flag for HOPS profile 2020-07-20 11:29:12 +02:00
Alexander Peltzer
a498e98342
Merge pull request #170 from jfy133/master 
Make walltimes more sophisticated and add a HOPS profile for nf-core/eager @ SHH
 2020-07-15 15:11:24 +02:00
James A. Fellows Yates
84e03b8264
Re-bump default walltimes after debugging/testing 2020-07-11 18:31:04 +02:00
James A. Fellows Yates
8f6409d144
Remove min support percent value to avoid confusion 2020-07-08 15:26:19 +02:00
James A. Fellows Yates
1af9ce293c
Update hops profile based on requests from pathogen group 2020-07-08 15:22:33 +02:00
James A. Fellows Yates
c57a404f18
Add desc for hops 2020-07-08 10:45:43 +02:00
jfy133
15dad7e2e7 Add caveats for EAGER @ SHH profiles 2020-07-08 09:47:03 +02:00
jfy133
926c14f7ee Cleverer process time submission 2020-07-08 09:36:56 +02:00
jfy133
563c27e1bb Try again to get better time resource submission 2020-07-08 09:36:28 +02:00
James A. Fellows Yates
c6905b609e
Update shh.config 2020-07-08 09:25:21 +02:00
James A. Fellows Yates
b360ce26bc
Update shh.config 2020-07-08 09:24:06 +02:00
James A. Fellows Yates
31edb4b5d7
Update shh.config 2020-07-08 09:20:00 +02:00
James A. Fellows Yates
aac3478e86
Add better task time values to account for large data 2020-07-08 09:12:11 +02:00
James A. Fellows Yates
737d826932
Update shh.config 2020-07-08 08:36:04 +02:00
piotr-faba-ardigen
ba24f1a1c8
Merge pull request #168 from piotr-faba-ardigen/add_bi_config 
Fix bi config
 2020-07-07 14:56:43 +02:00
James A. Fellows Yates
fcdbeaa446
Merge branch 'master' into master 2020-07-07 14:34:10 +02:00
James A. Fellows Yates
af01fccba1
Add a HOPS profile for nf-core/eager @ SHH 2020-07-07 14:31:11 +02:00
Piotr Faba
cb7a6f756a reduce complexity 2020-07-07 13:48:28 +02:00
James A. Fellows Yates
5517d2cbe0
Remove default non-profile bwa parameters from eager profile 
I realised today this is dangerous as these would not necessarily be reported if a user doesn't understand the profiles. Therefore removing these so nf-core/eager defaults are always used unless a specific profile (which would be described in the command itself) is explicitly named.
 2020-07-07 13:29:13 +02:00
Piotr Faba
4181184f58 fix spaces 2020-07-02 22:00:37 +02:00
Piotr Faba
4828e78708 fix error introduced earlier 2020-07-02 21:57:44 +02:00
James A. Fellows Yates
530da4d8c0
Merge pull request #167 from jfy133/master 
Bump number of eager @shh retries to account for deep sequencing data
 2020-06-30 11:33:29 +02:00
James A. Fellows Yates
c52428cd72
Bump number of eager @shh retries to account for deep sequencing data 2020-06-30 08:19:25 +02:00
Adrian
e375ad97ad reverting autoMounts due to bug 2020-06-26 13:39:37 +01:00
Phil Ewels
28027a8489 Prince config - use function to check if env SCRATCH is set 2020-06-26 14:22:32 +02:00
Phil Ewels
cd9fbb22dc
Merge pull request #161 from ewels/uct_hpc 
Update UCT hex -> hpc
 2020-06-22 09:18:43 +02:00
Alexander Peltzer
7774a6a8f3
Merge pull request #163 from piotr-faba-ardigen/add_bi_config 
resolve  #162 bug
 2020-06-19 08:57:44 +02:00
Piotr Faba
cb26bef3f3 resolve #162 bug 2020-06-18 20:30:05 +02:00
Phil Ewels
53e118210f Copy over HPC config 2020-06-17 15:20:22 +02:00
Phil Ewels
dbfcd7c5e9 Rename uct_hex > uct_hpc 2020-06-17 15:17:22 +02:00
Phil Ewels
17824d2d62 Merge czbiohub_aws_highpriority profile into czbiohub_aws 2020-06-16 15:20:39 +02:00
phue
6d356cc918 CBE: don't load singularity module 
singularity is now installed from CentOS repos, the environment module will be removed
 2020-06-05 12:07:26 +02:00
Alexander Peltzer
f877644059
Merge branch 'master' into master 2020-05-29 11:43:47 +02:00
Alexander Peltzer
32ec230098
Merge pull request #156 from piotr-faba-ardigen/add_bi_config 
Add bi config
 2020-05-27 21:03:15 +02:00
Piotr Faba
f139750bf4 print the error message before throwing Exception 2020-05-27 19:14:43 +02:00
Piotr Faba
3c695ba71c test error display 2020-05-27 18:00:47 +02:00
Alexander Peltzer
6011419454
Merge pull request #154 from jfy133/master 
Update SHH nf-core/eager group-specific profiles
 2020-05-27 17:52:09 +02:00
Piotr Faba
18d8edb046 add description and profile 2020-05-27 17:41:19 +02:00
Piotr Faba
66f191a1cf declate NXF_GLOBAL_CONFIG in ci 2020-05-27 16:30:00 +02:00
Piotr Faba
2685275952 switch include off 2020-05-27 16:24:47 +02:00
Piotr Faba
c31b03108c retry without Exception 2020-05-27 16:22:56 +02:00
Piotr Faba
1354ae4063 add bi config 2020-05-27 16:19:15 +02:00
James A. Fellows Yates
d070ed70d1
Update BWA settings based on feedback 2020-05-26 11:11:42 +02:00
James A. Fellows Yates
e31e781f29
Remove debugging 2020-05-26 11:07:06 +02:00
Harshil Patel
5981e5ec27
Merge pull request #153 from FriederikeHanssen/cfc_scratch 
Add scratch = true to avoid writing of intermediate file to /tmp
 2020-05-22 15:48:00 +01:00
James A. Fellows Yates
ff915ee504
Update shh.config 2020-05-12 12:47:59 +02:00
James A. Fellows Yates
8225e07819
Condensed base params and added names for debugging 2020-05-12 12:47:25 +02:00
James A. Fellows Yates
4814bac1c3
Fix sub-profiles 2020-05-12 12:42:42 +02:00
James A. Fellows Yates
38e9e54932
Merge pull request #151 from jfy133/master 
Add additional custom nf-core/eager params for SHH profile
 2020-05-07 09:25:02 +02:00
James A. Fellows Yates
cf6e697f0b
Further update aln based on modifications of EAGER defaults 2020-05-07 09:16:08 +02:00
James A. Fellows Yates
d42d7f4146
Sets the bwa aln parameter to 0.01 which is more commonly used at SHH 2020-05-04 21:02:16 +02:00
FriederikeHanssen
d6813d9c39 Add scratch = true to avoid writing of intermediate file to /tmp 2020-05-04 17:09:43 +02:00
MaxUlysse
e6f4d58fa6 update rnafusion munin specific config 2020-04-28 17:06:04 +02:00
Adrian
ad12bd4ad1 testing automounts 2020-04-28 16:03:06 +01:00
Harshil Patel
2300d5a962
Update genomes.config 2020-04-09 18:22:41 +01:00
MaxUlysse
50a44d037b better docs and organisation of giles 2020-04-09 17:02:36 +02:00
Maxime Garcia
34dc18faf6
Update uppmax.config 2020-04-09 11:35:37 +02:00
Adrian Larkeryd
405801638a icr_davros sarek config description 2020-04-08 11:56:17 +01:00
Adrian Larkeryd
78be4b358e icr_davros igenomes base 2020-04-08 11:55:16 +01:00
Maxime Garcia
d1ff87a416
Merge pull request #145 from bioatlas/master 
Adding UPPMAX specific config for ampliseq
 2020-03-31 15:46:21 +02:00
Daniel Lundin
c8de9be701 Adding UPPMAX specific config for ampliseq 2020-03-31 15:17:24 +02:00
MaxUlysse
db2dd4458b Merge remote-tracking branch 'upstream/master' into UPPMAX 2020-03-30 16:41:08 +02:00
MaxUlysse
8b570507cd update s 2020-03-30 16:40:11 +02:00
ggabernet
c81f693f73 add cfc_dev config 2020-03-23 17:16:34 +01:00
Olga Botvinnik
52369ba6ad
Add AaegL5.0 config 2020-03-17 16:45:20 -07:00
Maxime Garcia
123132d89a
Update munin.config 
fix typo
 2020-03-12 17:23:55 +01:00
Phil Ewels
5a3bdcca5b
Merge pull request #139 from Emiller88/utd 
fix(ganymede): use singularity/2.4.5
 2020-03-11 16:54:01 +00:00
Maxime Garcia
b6d52fdb89
Update conf/pipeline/sarek/munin.config 2020-03-11 15:48:29 +01:00
Maxime Garcia
0f34d757a9
Update munin.config 2020-03-11 15:48:17 +01:00
MaxUlysse
d24a296a01 add munin/rnafusion specific config 2020-03-11 14:02:01 +01:00
MaxUlysse
dd1ddf864b update sarek munin config 2020-03-11 14:01:28 +01:00
Edmund Miller
cece853663
fix(ganymede): use singularity/2.4.5 
Our 3.2.1 doesn't work right with snakemake or nextflow
 2020-03-10 21:03:24 -05:00
Edmund Miller
c42bb07981
fix: Singularity => singularity 
For some reason ours are lowercase
 2020-03-10 09:55:17 -05:00
Edmund Miller
123c44c56d
feat: add initial ganymede config 2020-03-09 16:18:41 -05:00
marcel-keller
8e3803e4d7
Update ebc.config 2020-03-09 16:57:45 +02:00
marcel-keller
c00bbe982b
Update ebc.config 2020-03-09 16:51:38 +02:00
marcel-keller
3b57519500
Update ebc.config 2020-03-09 16:48:50 +02:00
marcel-keller
de914e56ee
Create ebc.config 2020-03-09 16:08:01 +02:00
Evan Floden
d8ad376f71
Merge branch 'master' into master 2020-03-06 10:29:50 +00:00
Alexander Peltzer
59a787b179
Merge pull request #122 from marchoeppner/ccga-config 
Removing old CCGA profile from docs and linting
 2020-03-06 11:17:08 +01:00
mseybold
52842de88b
Update cfc.config 
test failed, so added the the default queue
 2020-03-06 10:46:37 +01:00
mseybold
8e42bbd7d0
Update cfc.config 
We just added some new HighMem nodes to the cfc, Partition/queue name is qbic, each node has 128Cores and 2TB of RAM.
The old queue (Name compute) is set to default by slurm.
Each process over 60GB of RAM or over 20cpus should run on those new nodes.
So added the queue State and adjusted the max_memory and max_cpu setting.
 2020-03-06 10:25:08 +01:00
Evan Floden
8a9d3ad8a0 First commit of Google Cloud config 2020-03-06 05:47:29 +00:00
phue
e2e4dd05d3 cbe: move container cache to different filesystem 
this is a workaround for squashfs errors that occur when containers are run from beeGFS
 2020-03-05 16:34:20 +01:00
Adrian Larkeryd
a67e77bb57 put comments back in correct format 2020-03-05 10:42:18 +00:00
Adrian Larkeryd
46223a3dbb remove comments 2020-03-05 10:39:19 +00:00
Adrian Larkeryd
ead67d1e90 description and contact 2020-03-05 09:24:10 +00:00
Adrian Larkeryd
a882b6cbaa adding icr_davros config files generic and sarek 2020-03-04 15:00:33 +00:00
James A. Fellows Yates
41a45187fa
Experiment to see if 'cleanup = true' works as expected 2020-03-03 16:47:49 +01:00
Maxime Garcia
9a8bb12020
Update conf/pipeline/sarek/uppmax.config 2020-02-27 17:22:03 +01:00
Maxime Garcia
8acbdacf03
Update conf/pipeline/sarek/uppmax.config 
Co-Authored-By: Johannes Alneberg <johannes.alneberg@scilifelab.se>
 2020-02-27 17:21:03 +01:00
Maxime Garcia
09ff8f5790
Update conf/pipeline/sarek/uppmax.config 2020-02-27 17:02:31 +01:00
Maxime Garcia
17d6a7e922
Update conf/pipeline/sarek/uppmax.config 2020-02-27 17:02:13 +01:00
Maxime Garcia
ab8998e12b
Update uppmax.config 2020-02-27 16:52:51 +01:00
MaxUlysse
a8d338d2aa Merge branch 'Uppmax' of github.com:MaxUlysse/nf-core_configs into Uppmax 2020-02-24 14:37:27 +01:00
MaxUlysse
9f74e88041 update file 2020-02-24 14:36:45 +01:00
Marc Hoeppner
6c5a5c8bcb Removing old CCGA profile from docs and linting 
Removing CCGA profile from master config

Removing CCGA profile from master config
 2020-02-24 12:16:33 +01:00
Maxime Garcia
9b897345da
Update conf/pipeline/sarek/uppmax.config 
Co-Authored-By: Phil Ewels <phil.ewels@scilifelab.se>
 2020-02-21 08:16:31 +01:00
Maxime Garcia
08e2804b37
Merge branch 'master' into Uppmax 2020-02-20 17:18:46 +01:00
MaxUlysse
aa905cd645 add UPPMAX specific sarek config 2020-02-20 17:14:18 +01:00
Daniel Straub
744db30da4
Update binac.config 
This is now close to optimal I think.
 2020-02-19 11:27:02 +01:00
marchoeppner
0830203b70 Adding new CCGA Med Cluster to profiles 
Updating README and fixing linting errors in CCGA_MED profile

Fixing order in profile queue and removed leading slash from readme for ccga profile docs

Fixing order in profile queue and removed leading slash from readme for ccga profile docs
 2020-02-11 11:12:51 +01:00
Daniel Straub
b7be65a31e
Cleanup config 2020-02-07 14:53:43 +01:00
Daniel Straub
7346bffdc8
Update binac.config 
Processes that ask for 128 Gb are queuing forever when on short queue, but executed when send to smp queue.
 2020-01-28 08:48:34 +01:00
James A. Fellows Yates
638758423a
Restricts MALT re-tries and hardcodes resources so cannot go above SDAG max 2019-12-21 20:55:54 +01:00
drpatelh
67c231d05c Change igenomes path 2019-12-18 10:54:23 +00:00
drpatelh
089b5b8e3b Update config 2019-12-12 13:44:37 +00:00
drpatelh
65c5668568 Update config 2019-12-12 13:02:44 +00:00
Maxime Garcia
d36172d4cf
Merge pull request #110 from MaxUlysse/MUNIN 
fix issue with withLabel selector
 2019-12-12 13:03:23 +01:00
MaxUlysse
2bf66514c5 fix issue with withLabel selector 2019-12-12 11:50:10 +01:00
Alexander Peltzer
a6d08ed646
Adjust custom pipeline config for ampliseq on BINAC 2019-12-11 16:09:44 +01:00
Alexander Peltzer
49cd35918a
Remove whitespace 2019-12-11 15:59:58 +01:00
Alexander Peltzer
5e6981d0ee
Export TZ in binac config 2019-12-11 15:59:25 +01:00