259 commits

Author	SHA1	Message	Date
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