438 commits

Author	SHA1	Message	Date
Maxime Garcia	9497b78149	Merge pull request #100 from MaxUlysse/UPPMAX ... Improve UPPMAX configs	2019-12-06 10:52:44 +01:00
Maxime Garcia	14864bb80b	Update conf/uppmax.config	2019-12-06 10:31:56 +01:00
Alexander Peltzer	da547b4ce3	Merge pull request #102 from phue/cbe_singularity ... cbe: load singularity/3.4.1	2019-12-06 10:21:55 +01:00
James A. Fellows Yates	0033b74e4e	Update shh.config	2019-12-05 18:08:39 +01:00
James A. Fellows Yates	dc0f1dfb40	Update shh.config	2019-12-05 17:58:49 +01:00
James A. Fellows Yates	b1a8b45aa0	Maybe typo?	2019-12-05 17:52:53 +01:00
jfy133	731372dac2	Added SHH specific EAGER configuration	2019-12-05 17:01:10 +01:00
phue	381c60e7b7	cbe: load singularity/3.4.1	2019-12-05 16:06:32 +01:00
MaxUlysse	a63ec24626	Merge branch 'UPPMAX' of github.com:MaxUlysse/nf-core_configs into UPPMAX	2019-12-05 15:18:04 +01:00
MaxUlysse	99afe86ea9	update docs	2019-12-05 15:18:01 +01:00
MaxUlysse	f41d325873	automatic configs work on all nodes	2019-12-05 15:07:59 +01:00
Maxime Garcia	78826c9d4e	Merge branch 'master' into UPPMAX	2019-12-05 12:52:34 +01:00
Alexander Peltzer	9cdb915efb	Merge pull request #101 from jfy133/master ... Condensing SHH profile(s) with sub-profiles	2019-12-05 12:51:31 +01:00
MaxUlysse	cf6e00d9f5	better match for hostname	2019-12-05 12:46:32 +01:00
MaxUlysse	20e451be3b	actually define hostname	2019-12-05 12:45:30 +01:00
MaxUlysse	0211b33a55	trying automatic configuration based on hostname	2019-12-05 12:41:18 +01:00
James A. Fellows Yates	842642a2bb	Apply suggestions from code review ... Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>	2019-12-05 12:23:36 +01:00
James A. Fellows Yates	678a3841b6	Update conf/shh.config ... Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>	2019-12-05 12:23:06 +01:00
jfy133	54dafbcfa3	Condensing SHH profiles following https://github.com/nf-core/configs/pull/100	2019-12-05 12:09:11 +01:00
MaxUlysse	cdbdbee0eb	replace -profile uppmax_devel by -profile uppmax,devel	2019-12-05 11:49:44 +01:00
Sabrina Krakau	2eed8f7429	Lowered max. memory for cfc	2019-11-28 12:49:02 +01:00
Olga Botvinnik	f57e00e87d	Set awsqueue parameter properly	2019-11-27 15:57:09 -08:00
Alexander Peltzer	4f77eae5cf	Mini adjustment for highmem queue on denbi	2019-11-27 14:23:01 +01:00
Maxime Garcia	2669401a72	Merge branch 'master' into sarek	2019-11-27 13:27:43 +01:00
Alexander Peltzer	5e0e3e0567	Merge pull request #96 from jfy133/master ... Splitting SHH config to one per cluster	2019-11-27 12:06:54 +01:00
Alexander Peltzer	54719c4761	Merge pull request #95 from ggabernet/master ... Update max memory for cfc profile	2019-11-26 21:21:07 +01:00
James A. Fellows Yates	c725c71e4d	Merge branch 'master' into master	2019-11-26 20:34:42 +01:00
jfy133	6f40c13473	Split shh config for each cluster	2019-11-26 20:20:17 +01:00
phue	88b5be3060	Merge branch 'master' of https://github.com/nf-core/configs into cbe_iGenomes	2019-11-26 18:08:43 +01:00
ggabernet	834f4b4179	updated memory cfc config	2019-11-26 17:30:41 +01:00
Alexander Peltzer	ee99d7f2d4	Merge pull request #94 from apeltzer/master ... Mini Cosmetic Fixes for README	2019-11-26 16:24:30 +01:00
Alexander Peltzer	b756ce54a4	Add genotoul fix	2019-11-26 16:09:08 +01:00
Alexander Peltzer	81739a3907	Merge pull request #93 from jfy133/master ... Updated max resources for SHH SDAG	2019-11-26 15:56:39 +01:00
James A. Fellows Yates	c3d27099ca	Updated authors	2019-11-26 15:26:05 +01:00
James A. Fellows Yates	ca6ddcadb0	Matching max CPUs to SDAG (supercruncher8)	2019-11-26 15:25:35 +01:00
MaxUlysse	6f638b7ad4	Merge branch 'sarek' of github.com:MaxUlysse/nf-core_configs into sarek	2019-11-26 15:22:02 +01:00
MaxUlysse	25f3bd68f8	container = null	2019-11-26 15:21:53 +01:00
Alexander Peltzer	5c39c1ed1a	Merge branch 'master' into master	2019-11-26 15:07:31 +01:00
Noirot Céline	611c318569	Update conf/genotoul.config ... Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>	2019-11-26 14:50:05 +01:00
Noirot Céline	dd4ff452da	Update conf/genotoul.config ... Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>	2019-11-26 14:49:47 +01:00
Alexander Peltzer	37c6714cc7	Nice prince	2019-11-26 14:29:52 +01:00
phue	bdf4a829b8	roll out iGenomes on cbe	2019-11-26 14:22:16 +01:00
Alexander Peltzer	23f9fd2d73	Merge branch 'master' into master	2019-11-26 14:20:36 +01:00
Maxime Garcia	68c709432f	Apply suggestions from code review ... Co-Authored-By: Phil Ewels <phil.ewels@scilifelab.se>	2019-11-26 14:17:32 +01:00
Alexander Peltzer	d592c79954	Merge branch 'master' into master	2019-11-26 13:59:06 +01:00
MaxUlysse	ebdfc2a768	fix container/module collision	2019-11-26 11:59:00 +01:00
Maxime Garcia	880551d246	Apply suggestions from code review	2019-11-26 11:58:13 +01:00
Maxime Garcia	f6c2e4c65f	Update docs/pipeline/sarek/munin.md ... Update conf/pipeline/sarek/munin.config testing out module and containers collision	2019-11-26 11:57:51 +01:00
Maxime Garcia	9d23f7a266	Update conf/pipeline/sarek/munin.config	2019-11-26 11:56:02 +01:00
MaxUlysse	45cec1ac2f	Add specific sarek config base, munin specific sarek config and docs ... rename file improve configs remove unnecessary params	2019-11-26 11:52:53 +01:00
MaxUlysse	028008c1d0	improve syntax	2019-11-26 11:48:29 +01:00
Maxime Garcia	93d5156c7d	Update conf/munin.config	2019-11-26 11:48:29 +01:00
MaxUlysse	e98f74e47b	actually belong to nf-core/configs/munin	2019-11-26 11:48:29 +01:00
MaxUlysse	edde1ee64d	fix container/module collision	2019-11-26 11:48:29 +01:00
Maxime Garcia	9a57e487d7	Apply suggestions from code review	2019-11-26 11:48:29 +01:00
Maxime Garcia	b029ccaa59	Update docs/pipeline/sarek/munin.md ... Update conf/pipeline/sarek/munin.config	2019-11-26 11:48:11 +01:00
Maxime Garcia	73047968cf	Update conf/pipeline/sarek/munin.config	2019-11-26 11:25:29 +01:00
MaxUlysse	cd1d0b5f8f	Add specific sarek config base, munin specific sarek config and docs ... rename file improve configs remove unnecessary params	2019-11-26 11:25:29 +01:00
Maxime Garcia	1ce8ce0c55	Apply suggestions from code review	2019-11-26 11:00:24 +01:00
MaxUlysse	75c1fd5cd9	fix tests	2019-11-26 10:43:23 +01:00
Alexander Peltzer	b60fa8109e	Shift some configs to params scope	2019-11-26 00:57:10 +01:00
Noirot Céline	ed4436c1a6	Merge branch 'master' into master	2019-11-25 16:24:12 +01:00
noirot	db51c49b2f	Add genotoul config	2019-11-25 14:54:25 +01:00
MaxUlysse	08a6b74825	add new profile to be shared: awsbatch	2019-11-19 14:16:06 +01:00
Alexander Peltzer	bc9ecf50ac	Update binac.config ... Upgrade to 3.4.2	2019-11-11 13:56:17 +01:00
Alexander Peltzer	e66ca6f670	Merge pull request #83 from nf-core/cfc_new_singularity_test ... Update Singularity to 3.4.2 on CFC	2019-11-11 13:55:01 +01:00
Alexander Peltzer	d2603a134e	Add in denbi cloud configs	2019-11-11 12:26:19 +01:00
Alexander Peltzer	426017d727	Merge remote-tracking branch 'upstream/master'	2019-11-11 12:21:53 +01:00
Alexander Peltzer	16a0ba9fd5	Update cfc.config	2019-11-08 10:06:23 +01:00
phue	5a9dbe5d7c	MENDEL is no more ... the cluster is no longer operational, was replaced by CBE	2019-10-28 14:11:34 +01:00
Alexander Peltzer	eb6d23254d	Fix binac resources	2019-10-28 13:22:12 +01:00
Alexander Peltzer	e557ced184	Update max memory	2019-10-28 13:21:41 +01:00
Alexander Peltzer	06bd1ab79e	Merge branch 'master' into master	2019-10-28 13:21:08 +01:00
Alexander Peltzer	41e607e7f9	Fix expression	2019-10-28 13:17:39 +01:00
Alexander Peltzer	494aa8b53e	Mini fix	2019-10-28 13:15:54 +01:00
Alexander Peltzer	5348b8c609	Revert "BINAC SMP / Short / Long Updates"	2019-10-28 13:12:31 +01:00
Alexander Peltzer	7951805fbf	Merge pull request #43 from apeltzer/master ... BINAC SMP / Short / Long Updates	2019-10-28 13:09:56 +01:00
Alexander Peltzer	83fcc0b2ba	Adjust max memory	2019-10-28 13:09:30 +01:00
phue	18ed48f398	deprecate igenomesIgnore in favor of igenomes_ignore ... keep both for now until all the pipelines have been synced	2019-10-28 11:38:24 +01:00
phue	123f199b68	cbe: dynamic qos logic	2019-10-27 20:44:08 +01:00
Alexander Peltzer	5ec19e3abb	Binac SMP / Long / Short Queue Additions	2019-10-27 13:28:00 +01:00
Maxime Borry	834601f05b	Merge branch 'master' of https://github.com/nf-core/configs	2019-10-25 15:52:23 +02:00
Maxime Borry	7a2fe44b43	resource based queuing	2019-10-25 15:50:49 +02:00
maxibor	5e54912ada	add queue choice	2019-10-25 14:08:02 +02:00
Anthony Bretaudeau	1f2786c78f	add genouest cluster	2019-10-16 18:15:04 +02:00
phue	9b3fda36f6	update singularity version ... singularity/3.1.0 is not available anymore	2019-10-10 21:22:19 +02:00
Sven Fillinger	dc3faf8a5f	Sends weblog messages over HTTPS	2019-10-10 12:56:39 +02:00
Sven Fillinger	855da0cee3	Refactors weblog url	2019-10-08 14:19:42 +02:00
Alexander Peltzer	ed8c9d9e7a	Update cfc.config	2019-10-08 13:20:58 +02:00
Alexander Peltzer	1e54d9510d	Update cfc.config	2019-10-08 13:15:49 +02:00
Alexander Peltzer	865909ac54	Update cfc.config	2019-10-08 13:14:21 +02:00
Alexander Peltzer	5fae33669d	Update cfc.config ... Try this out 👍	2019-10-08 13:07:28 +02:00
Alexander Peltzer	4555dd7d36	Update conf/cfc.config	2019-10-08 12:51:01 +02:00
Alexander Peltzer	abb6780081	Add Singularity Cache Directory	2019-10-08 12:48:24 +02:00
phue	5e257e7e9a	add cbe profile	2019-09-22 16:45:09 +02:00
Alexander Peltzer	836da97efd	Merge pull request #66 from marchoeppner/ccga-config ... Updating CCGA configs - adding cache dir and mount points	2019-09-03 17:25:34 +02:00
marchoeppner	3b638e9ccd	Fixing typo in ccga_dx config	2019-09-03 15:37:15 +02:00
Szilveszter Juhos	c3c0d088dd	typo	2019-08-16 11:13:32 +02:00
marchoeppner	486cdfce5f	Updating CCGA configs - adding cache dir and mount points	2019-08-07 13:19:16 +02:00
MaxUlysse	4183090379	fix: reduce cpu and mem usage	2019-08-07 12:26:51 +02:00
MaxUlysse	23dd3dd098	Merge branch 'master' of github.com:MaxUlysse/nf-core_configs	2019-08-07 11:56:52 +02:00
MaxUlysse	0bd19517b3	fix: typos	2019-08-07 11:55:56 +02:00
Maxime Garcia	d6a763214c	Update conf/munin.config ... Co-Authored-By: Harshil Patel <drpatelh@users.noreply.github.com>	2019-08-07 11:47:47 +02:00
Maxime Garcia	12fb2a60c5	Update conf/munin.config ... Co-Authored-By: Harshil Patel <drpatelh@users.noreply.github.com>	2019-08-07 11:47:41 +02:00
MaxUlysse	332ba0dadb	fix: update and rearrange munin configuration file and docs	2019-08-07 11:10:48 +02:00
Martin Proks	c583aa0233	Added kraken config (#15) ... * Added kraken template * docs: updated some info * fix: updated igenomes_base path	2019-08-05 11:19:05 +02:00
drpatelh	e0c684ee8f	Aarrrgh pulling configs from master	2019-07-31 23:39:42 +01:00
drpatelh	a692ded933	Remove workDir in czbiohub	2019-07-31 23:30:51 +01:00
drpatelh	daf1b9dcd2	Fix type in uppmax-devel	2019-07-31 22:09:30 +01:00
Remi Planel	1c0d596582	Merge remote-tracking branch 'upstream/master'	2019-07-30 16:15:20 +02:00
Remi Planel	b4cffe0455	Remove buggy cluster option	2019-07-30 15:15:07 +02:00
marchoeppner	b31db18dfb	Adding config file for CCGA dx cluster	2019-07-29 12:08:07 +02:00
Remi Planel	fbb33fde63	Details	2019-07-24 11:43:08 +02:00
Remi Planel	1b30c5a4d2	Add the Pasteur profile	2019-07-24 11:32:02 +02:00
Alexander Peltzer	9106559b2f	Update cfc.config	2019-07-15 17:53:11 +02:00
Olga Botvinnik	474e98daaf	Merge branch 'master' into olgabot/czb-update	2019-07-09 16:02:25 -07:00
marchoeppner	cb507177d5	Updating CCGA config file	2019-07-05 08:03:37 +02:00
Olga Botvinnik	069963ff8a	Make czbiohub_aws_highpriority only set the AWS Batch queue and nothing else	2019-07-03 16:01:47 -07:00
Olga Botvinnik	917ec0863d	add default trimming	2019-07-03 16:01:03 -07:00
Alexander Peltzer	45d36a1506	Update cfc.config ... Add Weblog for CFC cluster	2019-07-03 09:21:16 +02:00
Olga Botvinnik	6a2d2003f0	Add high priority AWS batch queue to CZBiohub AWS	2019-07-01 09:25:46 -07:00
Olga Botvinnik	70b5205d15	Add human salmon index and mouse star index	2019-06-27 15:02:47 -07:00
Olga Botvinnik	d1983f8acd	Use new and improved GENCODE+ERCC annotation	2019-06-26 17:56:26 -07:00
Olga Botvinnik	b0c67e0a9b	Add both seqCenter and seq_center	2019-06-24 17:52:10 -07:00
Olga Botvinnik	acad9ac7e5	Try to clean up czb update	2019-06-24 17:50:36 -07:00
Szilveszter Juhos	f40ed194e3	Using correct reference location for munin	2019-06-24 09:54:37 +02:00
James A. Fellows Yates	505af9a909	Merge pull request #49 from maxibor/master ... Fix queuesize Ccope and Singularity	2019-06-18 20:36:36 +02:00
maxibor	c7eed3fa4c	fix queuesize scope and singularity	2019-06-14 19:16:20 +02:00
Alexander Peltzer	ebe838ac7e	Merge pull request #45 from czbiohub/olgabot/czbiohub ... [WIP] Add CZ Biohub	2019-06-06 13:35:34 +02:00
Olga Botvinnik	3a481402b8	Get czbiohub config to work	2019-06-05 14:42:07 -07:00
Tobias Schraink	4491907f14	updated singularity version in conf/prince.config to reflect version installed on prince ... The prince admins changed the singularity version to 3.2.1 from 3.1.0, making the old version unavailable. To keep this config functional, I updated the version number for singularity.	2019-06-04 12:56:11 -04:00
Alexander Peltzer	515e9484de	Merge pull request #44 from drpatelh/dev ... Add proper nf-core logo	2019-06-01 12:36:57 +02:00
Olga Botvinnik	9c0315addb	Use flat nongzipped files	2019-05-31 13:17:48 -07:00
Olga Botvinnik	1b2fcf5a98	Add author lines	2019-05-31 08:16:51 -07:00
Olga Botvinnik	66eeeebe81	Initial commit of CZBiohub	2019-05-30 11:15:38 -07:00
Alexander Peltzer	441ddbcdab	Newest Update is 3.0.3	2019-05-28 15:25:10 +02:00
maxibor	de1b2aa7d2	remove autoformat added space	2019-04-25 15:50:48 +02:00
maxibor	efd831a8a3	add automounts for singularity	2019-04-25 15:48:20 +02:00
Alexander Peltzer	7d7c18273b	Merge pull request #41 from tobsecret/master ... Added configs for NYU clusters BigPurple (NYU Med) and Prince (NYU main campus) Last PR merge before Easter holiday ;-)	2019-04-19 00:13:49 +02:00
Tobias Schraink	4ba831705d	added nyu prince and bigpurple md files, added singularity cacheDir to prince and bigpurple configs	2019-04-18 14:13:02 -04:00
maxibor	9d9ac4c3bb	remove whitespace	2019-04-18 11:22:54 +02:00
maxibor	1772f4119c	adding igenomes to shh config	2019-04-18 11:19:53 +02:00
Tobias Schraink	4a915e330a	added warnings to run on SCRATCH	2019-04-17 17:15:16 -04:00
Tobias Schraink	51c2a54399	added nyu prince and bigpurple configs	2019-04-17 16:59:38 -04:00
maxibor	76a5fcf077	switch to queueSize 16 for shh config	2019-03-20 13:44:13 +01:00
maxibor	0929349303	add queueSize limited to 5	2019-03-18 11:13:11 +01:00
James A. Fellows Yates	ecb36dd8c2	Reduced memory and CPUs for cdag compatibility ... Also matches 'fair use' policy	2019-03-14 21:26:43 +01:00
James A. Fellows Yates	3da1373c14	Updated path to centralised singularity cache	2019-03-14 21:16:02 +01:00
Harshil Patel	8bc975c8c3	Merge pull request #33 from ewels/master ... Removed params.config_profile_name, added params.hostnames	2019-03-13 16:49:43 +00:00
Phil Ewels	1191863e1c	Removed params.config_profile_name, added params.hostnames	2019-03-13 17:19:34 +01:00
phue	13df59bfaf	remove singularity support ... reasons: * the kernel running on the compute nodes does not support overlayfs und thus containers downloaded from public registries won't run because they lack the /lustre mountpoint * building containers manually using the Singularity file would work, however nf-core pipelines will stop providing these files in future releases	2019-03-12 17:57:31 +00:00
Alexander Peltzer	fbf9397182	Bump	2019-03-12 18:48:29 +01:00
Alexander Peltzer	3ee7195fa8	Central resource for both binac and cfc now	2019-03-12 14:58:41 +01:00
Alexander Peltzer	68b759d6ef	Mini Update	2019-03-11 18:12:35 +01:00
Alexander Peltzer	f4f3c4e53b	Roll out binac too	2019-03-11 14:29:42 +01:00
Alexander Peltzer	6b21538062	Rolling out iGenomes now	2019-03-07 16:12:30 +01:00
phue	59887d9bc8	update config for MENDEL cluster	2019-02-27 16:03:26 +00:00
Alexander Peltzer	164ae59568	Update cfc.config ... Please use the newest singularity version 3.0.3!	2019-02-21 10:49:29 +01:00
Alexander Peltzer	d6ea834f40	Update cfc.config	2019-02-21 09:17:28 +01:00
Alexander Peltzer	637ffb782c	Fix CFC config	2019-02-19 17:03:53 +01:00
James A. Fellows Yates	7a51c684f5	Made small SLURM queue change for SHH	2019-01-21 20:31:37 +01:00
Martin Proks	7acd9cf7df	Updating suggested changes	2019-01-11 15:28:10 +01:00
Martin Proks	89dbb6c061	Setting Singularity as default method	2019-01-11 14:37:12 +01:00
Martin Proks	548c8bca3f	Updated munin doc and configuration	2019-01-10 15:46:16 +01:00
Martin Proks	f259178642	Added munin config boilerplate	2019-01-09 17:27:55 +01:00
Phil Ewels	66a08891c7	Documentation tweaks	2019-01-07 14:25:06 +01:00
Harshil Patel	59bc3b43be	Update crick.config	2019-01-07 11:35:49 +00:00
Harshil Patel	f81c67627e	Update crick.config	2019-01-07 11:18:01 +00:00
Alexander Peltzer	d4ea56aaae	Update UCT_Hex profile	2019-01-07 12:14:04 +01:00
Alexander Peltzer	2b814041ee	Add in both uppmax profiles	2019-01-04 16:33:54 +01:00
Alexander Peltzer	6f7a3cc422	Add Hebbe	2019-01-04 16:30:40 +01:00
Alexander Peltzer	e07d8bd687	Get rid of header in CRICK config	2019-01-04 16:29:49 +01:00
Alexander Peltzer	aca790bb4b	Add CCGA Profile	2019-01-04 16:28:41 +01:00
Alexander Peltzer	7af6b48b4d	Adjust general usage to separate params section	2019-01-04 14:55:22 +01:00
Alexander Peltzer	9c97680d4c	Add UZH	2019-01-04 14:49:52 +01:00
Alexander Peltzer	bc8e05f4b3	Add Phoenix	2019-01-04 14:48:14 +01:00
Alexander Peltzer	6ae7d02b14	Add Mendel	2019-01-04 14:46:30 +01:00
Alexander Peltzer	078272745a	Update BINAC, CFC, SHH COnfig profiles	2019-01-04 14:42:09 +01:00
Alexander Peltzer	87cea82c43	Use james github handle	2019-01-04 10:21:16 +01:00
Alexander Peltzer	a78fe147f0	Add more details on config profiles	2019-01-04 10:19:39 +01:00
Alexander Peltzer	1051339461	Remove base config stuff	2019-01-03 16:02:07 +01:00
Alexander Peltzer	98fca8a1ef	Add SHH Configuration	2019-01-03 16:01:06 +01:00
phue	5c609859c5	add config for MENDEL cluster	2018-12-04 16:58:33 +01:00
Harshil Patel	ddc0bbd7b3	Update phoenix.config	2018-11-26 23:31:44 +00:00
Alexander Peltzer	42ed4b9da4	Add Phoenix configs	2018-11-27 00:02:40 +01:00
Harshil Patel	2c513e5266	Update binac.config	2018-11-26 22:47:36 +00:00
Phil Ewels	e38e9327f4	Some tidying	2018-11-26 17:32:06 +01:00
drpatelh	d52db66077	Added existing configs from all pipelines	2018-11-23 15:56:34 +00:00