317 commits

Author	SHA1	Message	Date
Marc Hoeppner	6c5a5c8bcb	Removing old CCGA profile from docs and linting ... Removing CCGA profile from master config Removing CCGA profile from master config	2020-02-24 12:16:33 +01:00
Maxime Garcia	9b897345da	Update conf/pipeline/sarek/uppmax.config ... Co-Authored-By: Phil Ewels <phil.ewels@scilifelab.se>	2020-02-21 08:16:31 +01:00
Maxime Garcia	08e2804b37	Merge branch 'master' into Uppmax	2020-02-20 17:18:46 +01:00
MaxUlysse	aa905cd645	add UPPMAX specific sarek config	2020-02-20 17:14:18 +01:00
Daniel Straub	744db30da4	Update binac.config ... This is now close to optimal I think.	2020-02-19 11:27:02 +01:00
marchoeppner	0830203b70	Adding new CCGA Med Cluster to profiles ... Updating README and fixing linting errors in CCGA_MED profile Fixing order in profile queue and removed leading slash from readme for ccga profile docs Fixing order in profile queue and removed leading slash from readme for ccga profile docs	2020-02-11 11:12:51 +01:00
Daniel Straub	b7be65a31e	Cleanup config	2020-02-07 14:53:43 +01:00
Daniel Straub	7346bffdc8	Update binac.config ... Processes that ask for 128 Gb are queuing forever when on short queue, but executed when send to smp queue.	2020-01-28 08:48:34 +01:00
James A. Fellows Yates	638758423a	Restricts MALT re-tries and hardcodes resources so cannot go above SDAG max	2019-12-21 20:55:54 +01:00
drpatelh	67c231d05c	Change igenomes path	2019-12-18 10:54:23 +00:00
drpatelh	089b5b8e3b	Update config	2019-12-12 13:44:37 +00:00
drpatelh	65c5668568	Update config	2019-12-12 13:02:44 +00:00
Maxime Garcia	d36172d4cf	Merge pull request #110 from MaxUlysse/MUNIN ... fix issue with withLabel selector	2019-12-12 13:03:23 +01:00
MaxUlysse	2bf66514c5	fix issue with withLabel selector	2019-12-12 11:50:10 +01:00
Alexander Peltzer	a6d08ed646	Adjust custom pipeline config for ampliseq on BINAC	2019-12-11 16:09:44 +01:00
Alexander Peltzer	49cd35918a	Remove whitespace	2019-12-11 15:59:58 +01:00
Alexander Peltzer	5e6981d0ee	Export TZ in binac config	2019-12-11 15:59:25 +01:00
Alexander Peltzer	ac90acf470	Update envWhiteList for Binac Profile for testing purposes ... Add envWhitelist for TZ to fix https://github.com/nf-core/ampliseq/issues/114	2019-12-11 14:26:57 +01:00
James A. Fellows Yates	0beb98696f	Merge branch 'master' into master	2019-12-06 19:31:24 +01:00
James A. Fellows Yates	8747be8120	More tweaks, nextflow appears to add a little extra?	2019-12-06 19:27:16 +01:00
James A. Fellows Yates	5c6760b2f0	Tweak back again	2019-12-06 19:25:07 +01:00
James A. Fellows Yates	46f6d20a77	Put parameters back to correct levels	2019-12-06 19:13:29 +01:00
James A. Fellows Yates	18931763fa	Add space?	2019-12-06 19:11:08 +01:00
James A. Fellows Yates	f59443daf0	Update shh.config	2019-12-06 19:09:20 +01:00
James A. Fellows Yates	1ab1370872	Try to make resources satisfiable	2019-12-06 19:06:05 +01:00
James A. Fellows Yates	6e596d1730	Fix stupid wrong bracket typo -.-	2019-12-06 18:37:39 +01:00
James A. Fellows Yates	b28e1a0905	Wrong bracket typo fix -.-	2019-12-06 18:34:18 +01:00
Alexander Peltzer	1f7940c2ee	Merge pull request #104 from jfy133/master ... Attempt to fix process specific configs with pipeline specific configs	2019-12-06 17:16:37 +01:00
jfy133	e8b4675692	Cleanup and tweaking	2019-12-06 13:17:31 +01:00
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