947 commits

Author	SHA1	Message	Date
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
Brad Langhorst	ac4372b610	adds varskip	2021-08-03 13:46:17 -04:00
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	937538d160	Fix typo in file path	2021-07-23 10:18:24 +01:00
ameynert	238d6e5e96	Added cacheDir to singularity in eddie profile	2021-07-23 09:33:02 +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