931 commits

Author	SHA1	Message	Date
Praveen Raj S	cb96c4bd2d	Update conf/munin.config ... Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>	2022-03-15 16:56:11 +01:00
Praveen Raj S	13c66f7e98	Update conf/munin.config ... Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>	2022-03-15 16:56:03 +01:00
Praveen Raj S	50c4610345	Adjusted time and maxforks for Mutect2	2022-03-15 16:29:19 +01:00
Alexander Peltzer	3e4fae71a4	Merge branch 'master' into fix-show-profiles	2022-03-15 14:52:29 +01:00
James A. Fellows Yates	1b5037ce5e	Update eva.config	2022-03-15 07:49:06 +01:00
James A. Fellows Yates	1565b2ce63	Update eva.config	2022-03-15 07:42:23 +01:00
James A. Fellows Yates	f725b6c431	Apply suggestions from code review	2022-03-15 07:36:34 +01:00
Nathan S. Watson-Haigh	a0f5ac7445	Added references subdir to igenomes_base	2022-03-15 11:41:51 +10:30
James A. Fellows Yates	4670f8bf0c	Update eva.config	2022-03-14 14:56:01 +01:00
James A. Fellows Yates	a2e2e94333	Merge pull request #344 from njspix/vai ... Add VAI configuration	2022-03-14 14:36:00 +01:00
Nathan Watson-Haigh	cc55026751	Add singularity to PATH	2022-03-13 07:39:31 +10:30
Nathan Watson-Haigh	2f0b022571	Fixed typos	2022-03-13 00:08:42 +10:30
Nathan Watson-Haigh	b638694bd0	Added SAHMRI HPC profile	2022-03-12 21:17:33 +10:30
Matiss	6c79c75eec	Merge pull request #290 from maxozo/master ... added leicester profile	2022-03-11 09:21:09 +00:00
Nathan Spix	d067f61329	remove extra spaces	2022-03-07 15:22:18 -05:00
Spix	17c77ad516	update singularity command	2022-03-07 15:13:26 -05:00
Spix	c97c48ae5b	update singularity command	2022-03-07 15:11:45 -05:00
Spix	429c7b4fa8	initial commit	2022-03-07 15:01:46 -05:00
Alexander Peltzer	d0d86bfb2a	Merge pull request #339 from jfy133/rnaseq_mpcdf ... Add RNASEQ specific config for MPCDF	2022-03-07 13:59:08 +01:00
James A. Fellows Yates	975fca6721	Apply suggestions from code review	2022-03-07 13:51:00 +01:00
Natalia Zajac	97058995ef	Update on singularity cache	2022-03-07 12:37:01 +01:00
Natalia Zajac	e07a0e548e	Config Addition	2022-03-04 12:16:01 +01:00
James Fellows Yates	70318c3b2a	Tweak eager settigs	2022-03-03 14:29:30 +01:00
James A. Fellows Yates	546393ed18	Apply suggestions from code review	2022-03-03 14:22:35 +01:00
ilight1542	5a0543e4ac	Merge branch 'rnaseq_mpcdf' into mpcdf_eager_config_update	2022-03-03 14:17:18 +01:00
ilight1542	25c644abb7	modified mpcdf configs (general + eager)	2022-03-03 13:55:02 +01:00
James Fellows Yates	7112e74b73	Tweak settings based on latest batch specs	2022-03-03 13:43:40 +01:00
James A. Fellows Yates	17312604cf	Update mpcdf.config	2022-03-03 12:25:06 +01:00
James Fellows Yates	94f8cbcb84	Add rnaseq pipeline specific config for MPCDF	2022-03-03 12:20:02 +01:00
James A. Fellows Yates	5547e45ab5	Merge branch 'master' into jfy133-patch	2022-03-02 08:28:22 +01:00
James A. Fellows Yates	ea052a7b67	Merge pull request #334 from jfy133/eva-update ... eva: generalise custom SGE mem flag	2022-03-01 09:23:04 +01:00
James A. Fellows Yates	a6c12d8edc	Merge pull request #322 from U-BDS/master ... Add UAB Cheaha profile	2022-03-01 08:29:54 +01:00
PCQ	1ff92db608	Merge branch 'nf-core:master' into master	2022-02-28 14:50:41 +01:00
James A. Fellows Yates	89f6484325	Merge pull request #319 from maltesemike/patch-2 ... Update mpcdf.config	2022-02-28 14:06:06 +01:00
James A. Fellows Yates	46f046d477	Update eva.config	2022-02-28 14:00:37 +01:00
James A. Fellows Yates	d7d9951dbf	Insert h_vmem for all nf-core pipelines	2022-02-28 14:00:16 +01:00
James A. Fellows Yates	6210ee874c	Update eva.config	2022-02-28 13:57:37 +01:00
Mei Wu	dcba537d15	picard md is single threaded	2022-02-21 16:19:17 +01:00
Maxime U. Garcia	41e00ae8f9	Update conf/munin.config	2022-02-14 13:11:46 +01:00
Praveen Raj S	90936a5518	Added: runOptions to singularity ... To bind external mount directories at runtime.	2022-02-14 12:45:20 +01:00
Combiz Khozoie	2d434c6ee5	Merge pull request #321 from nf-core/combiz-patch-1 ... Imperial config updates	2022-02-11 14:49:30 +00:00
Maxime U. Garcia	4a936a685e	Merge pull request #317 from nf-core/praveenraj2018-patch-1 ... Added genome parameter	2022-02-11 15:33:18 +01:00
Combiz Khozoie	a77f718ae2	Merge pull request #330 from nf-core/master ... Pulling master to branch	2022-02-11 14:18:01 +00:00
Combiz Khozoie	3ce32f50c4	Update imperial.config ... Moved params configs from internal profile to universal	2022-02-11 11:02:40 +00:00
Combiz Khozoie	b99b74b2d3	Update imperial.config ... Fixed indent	2022-02-11 00:26:45 +00:00
Combiz Khozoie	38a05a6531	Update imperial.config ... Reworked to use internal profiles for the Imperial HPC and the MedBio cluster.	2022-02-10 23:46:14 +00:00
Combiz Khozoie	e1d0bf0cd2	Delete imperial_mb.config ... Separate config for the medbio queue now deprecated in favour of an internal profile within the main imperial.config	2022-02-10 23:44:49 +00:00
Combiz Khozoie	fe5474a029	Update imperial.config ... Multiple process level updates reflecting the latest job sizing guidelines for the Imperial HPC	2022-02-10 23:02:47 +00:00
Harshil Patel	8fa6ab9b35	Merge pull request #323 from stevin-wilson/patch-1 ... Added ARTIC v4.1 primer set information	2022-02-10 19:17:47 +00:00
James Fellows Yates	88ddc9eee7	fffff	2022-02-10 11:34:57 +01:00
James Fellows Yates	d7d0f5cecc	Change base time	2022-02-10 11:32:49 +01:00
James Fellows Yates	dbd78f8075	Re add .	2022-02-10 11:26:18 +01:00
James Fellows Yates	dd94895f16	remove quotes	2022-02-10 11:22:45 +01:00
James Fellows Yates	39c2d9b25b	Oops	2022-02-10 11:19:16 +01:00
James Fellows Yates	c0ee3225ad	Add times for 365d	2022-02-10 11:02:52 +01:00
Thiseas C. Lamnidis	fa4075c2a0	Removed all time limits	2022-02-10 10:00:18 +01:00
James A. Fellows Yates	64355b84d2	Merge pull request #325 from jfy133/eva-update ... Read add empty BAM exit code for qualimap 255 for eager @ EVA	2022-02-08 11:28:36 +01:00
James A. Fellows Yates	2b06293f64	Read add empty BAM exit code for qualitmap 255	2022-02-08 11:15:17 +01:00
James A. Fellows Yates	8d286e3b69	Merge pull request #324 from jfy133/eva-update ... New attempt of workaround SGE + Java incompatibility for eager @ EVA	2022-02-06 20:02:03 +01:00
James A. Fellows Yates	8c5a54ac9f	Update conf/pipeline/eager/eva.config	2022-02-06 19:37:53 +01:00
James A. Fellows Yates	aa525c6ebf	Allow exit code 1 retry for all java processes	2022-02-06 09:07:53 +01:00
Stevin Wilson	dbb71161c5	Added ARTIC v4.1 primer set information	2022-02-04 15:31:51 -05:00
phue	7bf6f284fa	cbe: lower the threshold for switching to m queue	2022-02-04 10:33:00 +01:00
phue	49810a69b3	cbe: add gpu support ... just in case.. note that this will need --nv in containerOptions in order to mount cuda libs into the container	2022-02-04 10:31:58 +01:00
phue	52b6f7da21	update anaconda module ... not sure why a binary distribution needs a buildenv at all, but well	2022-02-04 10:18:59 +01:00
James A. Fellows Yates	81fe720b00	Update eva.config	2022-02-04 09:31:33 +01:00
James A. Fellows Yates	86a9042eac	Update eva.config	2022-02-04 09:25:01 +01:00
Combiz Khozoie	81a273c730	Update imperial_mb.config ... Dropped support for pqmedbio-large which is not currently available.	2022-02-03 18:31:02 +00:00
Combiz Khozoie	2bdf5863d9	Update imperial.config ... Removed my contact details. Users can request help on the nf-core slack.	2022-02-03 18:28:11 +00:00
Combiz Khozoie	731f86e7f1	Update imperial_mb.config ... Removed my contact details. Users can request help on the nf-core slack.	2022-02-03 18:27:49 +00:00
Combiz Khozoie	453080f282	Update imperial.config ... Removed my contact details. Users can request help on the nf-core slack.	2022-02-03 18:26:30 +00:00
James A. Fellows Yates	50aafc6410	Update eva.config	2022-02-03 17:03:10 +01:00
James A. Fellows Yates	e02196d6ad	Update eva.config	2022-02-03 17:02:34 +01:00
James A. Fellows Yates	0e41349324	Update eva.config	2022-02-03 17:01:54 +01:00
Michael Borg	cc380ce9a1	Update mpcdf.config ... Added polling frequencies to the config as requested by MPCDF admin. Also updated the number of (real) cores on Raven.	2022-02-02 13:33:03 +01:00
James Fellows Yates	2562a2f563	Remove virtual free	2022-02-02 08:06:00 +01:00
James A. Fellows Yates	8739aabbf0	Bump markduplicates by default	2022-02-02 08:00:13 +01:00
Austyn Trull	1c9e1bf8a1	Fixing syntax in cheaha profile	2022-01-28 14:18:57 -06:00
Lara Ianov	9c0d550222	max_memory increase to reflect largemem	2022-01-28 11:45:13 -06:00
Austyn Trull	06541411dd	Initial commit of cheaha profile	2022-01-28 11:37:42 -06:00
Harshil Patel	9792226f5c	Update genomes.config	2022-01-27 12:45:41 +00:00
Praveen Raj S	5c1afd56bf	Added genome parameter ... Added genome parameter to the config file	2022-01-20 22:25:31 +01:00
Harshil Patel	cd6b8e0f17	Add --nextclade_dataset params	2022-01-17 16:51:55 +00:00
Harshil Patel	f26c465bd4	Add Nextclade genome details to viralrecon genome config	2022-01-17 11:27:10 +00:00
James A. Fellows Yates	5fd5c43906	Update eva.config	2022-01-14 07:03:05 +01:00
Maxime U. Garcia	61682f33b3	Merge pull request #310 from nf-core/praveenraj2018-patch-1 ... Updated sentieon version through a new module file	2022-01-10 12:04:20 +01:00
ameynert	0f56588acc	Added memory & cluster options specification for eddie sarek config	2022-01-06 10:15:34 +00:00
Kevin Brick	94d5a1b5f2	Update nihbiowulf.config	2021-12-23 15:36:38 -05:00
praveenraj2018	53ab5ee34f	Updated sentieon version through a new module file ... A local module file has been created to run the latest version of Sentieon. Doing this change, as the new version of Sentieon has only a dependency library update, hence it should not break the Sentieon pipeline. Tested locally with a test.conf having the new process block.	2021-12-21 15:21:59 +01:00
Kevin Brick	1abb1c2d95	Merge pull request #309 from kevbrick/master ... Added config for NIH Biowulf Cluster	2021-12-20 13:05:19 -05:00
Kevin Brick	82c7d553a7	Update bind-paths	2021-12-20 11:29:09 -05:00
Kevin Brick	87e4ece034	Add files via upload	2021-12-17 00:36:51 -05:00
Venkat Malladi	306c802b4e	Fix name of Params	2021-12-16 09:27:23 -06:00
PCQ	698555f801	Rename marvin.conf to marvin.config	2021-12-15 14:44:05 +01:00
praveenraj2018	0557f4e062	Renamed star_index directory	2021-12-14 21:15:12 +01:00
Maxime U. Garcia	5e92e2ef11	Update conf/pipeline/rnavar/munin.config	2021-12-14 16:10:31 +01:00
Praveen	cc1fe5b5a0	Addressed review feedback	2021-12-14 03:58:54 +01:00
Praveen	b4d5330c0e	Added rnavar pipeline config for Munin	2021-12-14 03:52:37 +01:00
PCQ	3a61adb69b	Rename Marvin.conf to marvin.conf	2021-12-13 11:38:48 +01:00
PCQ	50d90cd686	Marvin Cluster addition ... Added the config for the Marvin cluster of the Universitat Pompeu Fabra (UPF)	2021-12-10 17:11:43 +01:00
James A. Fellows Yates	55f452d81e	Update eva.config	2021-12-07 09:27:28 +01:00
James Fellows Yates	e8252ad61c	Reintroduce bionode8, bump overhead for flagstat	2021-12-03 08:36:31 +01:00
James Fellows Yates	06b40798c0	Exclude bionode8	2021-12-02 10:35:35 +01:00
Phil Ewels	4785ceccba	Merge pull request #245 from ikeller/unibe_ibu ... Unibe ibu	2021-11-19 00:56:25 +01:00
Phil Ewels	291fcb20a5	Merge pull request #297 from vsmalladi/azure ... Add in template for Azure Workflow	2021-11-19 00:55:54 +01:00
Venkat Malladi	72ccd44ad6	Remove storage name.	2021-11-18 17:52:51 -06:00
Venkat Malladi	ed4c1d5f22	Remove work_dir option.	2021-11-18 17:52:24 -06:00
Phil Ewels	e090bbd5fe	Merge pull request #241 from asafpr/master ... replaced owner in JAX	2021-11-19 00:03:11 +01:00
Phil Ewels	a26b3bf1e3	Merge branch 'master' into unibe_ibu	2021-11-19 00:02:30 +01:00
Phil Ewels	15080d958e	Merge pull request #283 from aunderwo/master ... change max_time diretcive in the correct place	2021-11-19 00:00:52 +01:00
Venkat Malladi	13a8d7aebe	Fix spelling.	2021-11-18 15:51:12 -06:00
Venkat Malladi	845a9ce971	Update Readme with more inforamtion on the options.	2021-11-18 15:47:27 -06:00
Venkat Malladi	219244f1b4	Add in sample datastorage for Illumina Platinum genomes.	2021-11-18 15:28:34 -06:00
Venkat Malladi	b1a9c2e4c6	Add in fake key.	2021-11-18 15:20:59 -06:00
Venkat Malladi	a8075ee938	Fix configuration to pass.	2021-11-18 15:15:23 -06:00
Venkat Malladi	237f91a3b7	Add in minmum config for azure.	2021-11-18 14:51:39 -06:00
Harshil Patel	a098ad9e06	Add Chris as main contact at The Crick	2021-11-03 11:11:05 +00:00
Phil Ewels	501db6bd2b	Update conf/uppmax.config ... Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>	2021-11-02 23:55:27 +01:00
Phil Ewels	c842ca70a7	Address review comments	2021-11-02 13:32:19 +01:00
Phil Ewels	9a17fdb6d9	Update conf/uppmax.config ... Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>	2021-11-02 09:58:04 +01:00
Phil Ewels	c7dc9aa892	UPPMAX profile - minor tweaks ... * Only one params block instead of two * Return only one 'grep' result and don't pipe to 'head' * Use .startsWith instead of regex matching * Print detected cluster name in the profile description	2021-11-02 09:15:01 +01:00
Pontus Freyhult	a04b5079f0	Make memory checks use closed intervals	2021-11-02 07:55:52 +01:00
Matiss Ozols	d45a06a681	added leicester profile	2021-10-21 19:02:13 +01:00
Matiss Ozols	e8ce4fe8df	added leicester profile	2021-10-21 18:59:17 +01:00
Matiss Ozols	f8b932ae2d	added leicester profile	2021-10-21 18:32:57 +01:00
James A. Fellows Yates	ffdb0a937f	Take previous working one I think	2021-10-18 10:58:06 +02:00
James A. Fellows Yates	b269a577e6	Revert 1240k	2021-10-18 10:52:28 +02:00
Thiseas C. Lamnidis	e741ecb7a7	Update eva.config	2021-10-13 13:04:41 +02:00
Thiseas C. Lamnidis	92648c1c1f	added 1240k profile	2021-10-12 15:12:49 +02:00
Mahesh Binzer-Panchal	ac815ce790	Merge branch 'master' into add_snic_tmp	2021-10-11 09:57:49 +02:00
Pontus Freyhult	33ae41bc91	Merge pull request #226 from pontus/master ... UPPMAX: Allow jobs needing more memory than thin nodes, pick up cluster info through slurm	2021-10-10 12:05:07 +02:00
James A. Fellows Yates	73b6b74c69	Merge pull request #279 from pierrespc/master ... Added Configuration files for running in Maestro HPC at Pasteur Institute, Paris	2021-10-08 19:15:47 +02:00
Mahesh Binzer-Panchal	747a89b4c5	Update conf/uppmax.config	2021-10-08 13:40:59 +02:00
pierrespc	035ab61f61	added unlimitedtime profile to maestro; changed cache for bwa process	2021-10-08 09:05:46 +02:00
Mahesh Binzer-Panchal	e557e94bfb	Add SNIC_TMP to config	2021-10-07 16:05:03 +02:00
FriederikeHanssen	f1756ba121	Merge branch 'nf-core:master' into cfc	2021-10-04 18:04:18 +02:00
pierrespc	1621585558	improving documentation	2021-10-04 16:08:33 +02:00
pierrespc	e5d4a357c5	clean doc	2021-10-04 15:08:01 +02:00
Falko Hofmann	0950eb3518	Merge pull request #251 from phue/cbe_singularity_workaround ... cbe: send SIGUSR2 upon job termination	2021-10-04 13:24:53 +02:00
Rike	f6e16f2872	Add check_resource to respect max_resource/max_cpus	2021-10-04 10:14:02 +02:00
pierrespc	f6266879d6	edited maestronuclear and maestromitocondrial configs. The latter has not been optimized yet	2021-09-29 13:47:35 +02:00
pierrespc	b71df6fe57	renamed eager pipeline config file	2021-09-29 13:22:07 +02:00
pierrespc	9ea3e2096a	long and normal qos profiles defined now in an unique maestro config file. maestro.config also defined in pipeline/eager for ressources assignation to specific processes	2021-09-29 13:11:14 +02:00
Bjørn Peare Bartholdy	e750a6d445	Update conf/alice.config ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>	2021-09-28 13:34:12 +02:00
Bjørn Peare Bartholdy	197bd6cfb1	Merge branch 'nf-core:master' into master	2021-09-28 12:09:50 +02:00
bbartholdy	b6ccb46383	add ALICE profile	2021-09-28 12:08:27 +02:00
Mei Wu	79a79f7d8d	added pipeline-specific config	2021-09-28 10:38:25 +02:00
Mei Wu	c2d74b290a	fix md	2021-09-27 16:25:02 +02:00
Mei Wu	a8a2027f70	Merge branch 'master' into hasta	2021-09-27 16:12:23 +02:00
Mei Wu	06fac1dcfc	initial commit	2021-09-27 16:05:32 +02:00
Mei Wu	ae0adb056f	initial commit	2021-09-27 16:05:19 +02:00
Anthony Underwood	7469e20b4e	change max_time diretcive in the correct place	2021-09-25 09:23:24 +01:00
Anthony Underwood	6a970dc4a8	update max time for long queue	2021-09-23 11:59:45 +01:00
Patrick Hüther	1cbe2759c4	fix invalid rapid qos selection ... it only applies to the c partition	2021-09-22 11:54:27 +02:00
pierrespc	3e22b85b02	maestro only for normal qos	2021-09-22 10:13:46 +02:00
Anthony Underwood	50df2105fb	update long jobs to be submitted to the long queue	2021-09-21 14:42:59 +01:00
pierrespc	3b593d46ec	merged two pasteur config files for maestro	2021-09-20 15:14:50 +02:00
Harshil Patel	5068e4806f	Merge pull request #271 from theoportlock/master ... Adds Rosalind config for KCL!	2021-09-17 13:36:19 +01:00
Harshil Patel	3b95fd9ee3	Update conf/rosalind.config	2021-09-17 13:15:09 +01:00
theoportlock	9116a09afe	Fixes formatting and ignore_params	2021-09-17 13:21:32 +02:00
pierrespc	4614ff6f45	change max mem in Normal	2021-09-16 16:50:45 +02:00
pierrespc	de2a745fde	change type in Normal name	2021-09-16 16:48:26 +02:00
pierrespc	482e7cf8de	2 config files for Maestro HPC at Pasteur Institute, Paris	2021-09-16 12:40:56 +02:00
Marc Trunjer Kusk Nielsen	a55c3c04eb	Update computerome.config ... Adding genomes and modules back into schema_ingore_params to avoid warnings about unexpected parameters.	2021-09-15 19:54:51 +02:00
Marc Trunjer Kusk Nielsen	8b29b5584e	Update computerome.config	2021-09-15 14:20:02 +02:00
Marc Trunjer Kusk Nielsen	ab8a9ad0b8	Update computerome.config	2021-09-15 13:27:23 +02:00
theoportlock	9c97220919	Merge branch 'master' of https://github.com/theoportlock/configs	2021-09-15 11:43:09 +02:00
theoportlock	3c86f8f47c	Removes the broken clusterOptions	2021-09-15 11:42:43 +02:00
Marc Trunjer Kusk Nielsen	aad70fe86d	Merge branch 'nf-core:master' into computerome	2021-09-15 11:08:48 +02:00
Marc Trunjer Kusk Nielsen	29003e13f1	Update computerome.config	2021-09-15 10:22:57 +02:00
James A. Fellows Yates	a7b1183065	Remove 1CPU for host removal fastq	2021-09-14 11:52:21 +02:00
Marc Trunjer Kusk Nielsen	86e21b378a	Update computerome.config	2021-09-13 14:26:10 +02:00
Marc Trunjer Kusk Nielsen	275288632d	Update computerome.config	2021-09-13 14:22:22 +02:00
Marc Trunjer Kusk Nielsen	366f945a40	Update computerome.config	2021-09-13 14:20:55 +02:00
Marc Trunjer Kusk Nielsen	8ebdd43898	Update computerome.config	2021-09-13 14:01:35 +02:00
Marc Trunjer Kusk Nielsen	1071eb9d2e	Update computerome.config	2021-09-13 13:38:46 +02:00
Marc Trunjer Kusk Nielsen	2e515dc861	Update computerome.config ... Don't raise an error when --project is specified	2021-09-13 13:38:25 +02:00
Marc Trunjer Kusk Nielsen	e5cba18c9b	Update computerome.config	2021-09-13 13:28:33 +02:00
Marc Trunjer Kusk Nielsen	0327ef40ea	Update computerome.config	2021-09-13 13:20:57 +02:00
Marc Trunjer Kusk Nielsen	a0ba05fd99	Update computerome.config	2021-09-13 08:36:30 +02:00
Marc Trunjer Kusk Nielsen	84f94d92c4	Update computerome.config ... Added a way to use `--project` to provide project information to the scheduler. Inspired by the uppmax config	2021-09-10 15:10:19 +02:00
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