756 commits

Author	SHA1	Message	Date
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
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