281 commits

Author	SHA1	Message	Date
Evan Floden	8a9d3ad8a0	First commit of Google Cloud config	2020-03-06 05:47:29 +00:00
phue	e2e4dd05d3	cbe: move container cache to different filesystem ... this is a workaround for squashfs errors that occur when containers are run from beeGFS	2020-03-05 16:34:20 +01:00
Adrian Larkeryd	a67e77bb57	put comments back in correct format	2020-03-05 10:42:18 +00:00
Adrian Larkeryd	46223a3dbb	remove comments	2020-03-05 10:39:19 +00:00
Adrian Larkeryd	ead67d1e90	description and contact	2020-03-05 09:24:10 +00:00
Adrian Larkeryd	a882b6cbaa	adding icr_davros config files generic and sarek	2020-03-04 15:00:33 +00:00
James A. Fellows Yates	41a45187fa	Experiment to see if 'cleanup = true' works as expected	2020-03-03 16:47:49 +01:00
Maxime Garcia	9a8bb12020	Update conf/pipeline/sarek/uppmax.config	2020-02-27 17:22:03 +01:00
Maxime Garcia	8acbdacf03	Update conf/pipeline/sarek/uppmax.config ... Co-Authored-By: Johannes Alneberg <johannes.alneberg@scilifelab.se>	2020-02-27 17:21:03 +01:00
Maxime Garcia	09ff8f5790	Update conf/pipeline/sarek/uppmax.config	2020-02-27 17:02:31 +01:00
Maxime Garcia	17d6a7e922	Update conf/pipeline/sarek/uppmax.config	2020-02-27 17:02:13 +01:00
Maxime Garcia	ab8998e12b	Update uppmax.config	2020-02-27 16:52:51 +01:00
MaxUlysse	a8d338d2aa	Merge branch 'Uppmax' of github.com:MaxUlysse/nf-core_configs into Uppmax	2020-02-24 14:37:27 +01:00
MaxUlysse	9f74e88041	update file	2020-02-24 14:36:45 +01:00
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