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436 commits

Author SHA1 Message Date
Gisela Gabernet
4e9e5d2c67
Merge branch 'master' into cfc_sarek 2021-04-23 16:47:04 +02:00
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
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
Phil Ewels
2f77d16b70
Merge pull request #220 from ewels/master 
UPPMAX: Avoid undefined parameter warnings
 2021-04-08 15:06:00 +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
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