458 commits

Author	SHA1	Message	Date
Combiz Khozoie	17cf4e3b35	fixed indents	2020-12-18 15:34:56 +00:00
Combiz Khozoie	3824403b4e	removed workDir from Imperial configs	2020-12-18 10:31:36 +00:00
Combiz Khozoie	a61992d144	Added institutional configs for Imperial and Imperial MEDBIO. Added institutional pipeline configs for scflow for Imperial and Imperial MEDBIO	2020-12-18 10:21:26 +00:00
marcel-keller	c9ceaff3b3	change of directory for conda environments ... change of directory due to recent changes in our infrastructure	2020-12-09 15:11:21 +02:00
emnilsson	8cc2fc5ecb	Merge pull request #193 from emnilsson/master ... Modified ampliseq-specific uppmax-config	2020-12-02 13:40:43 +01:00
Alexander Peltzer	99985c658f	Merge pull request #194 from marcel-keller/ebc ... Update ebc.config	2020-11-26 14:12:33 +01:00
marcel-keller	5590a9743a	Update ebc.config ... queueSize to 64	2020-11-26 15:05:25 +02:00
Emelie Nilsso	febf38dd8e	Removed an old process so that only relevant processes are included	2020-11-26 13:38:47 +01:00
Emelie Nilsso	d61ed01d2d	Updated process names according to ampliseq main.nf	2020-11-25 17:50:30 +01:00
Emelie Nilsso	37e7cfae2c	Removed unnecessary code that was used to troubleshoot	2020-11-24 07:14:23 +01:00
Emelie Nilsso	cd59bba83e	Merge branch 'master' of https://github.com/nf-core/configs	2020-11-24 07:10:05 +01:00
Emelie Nilsso	c47088cda2	Merge remote-tracking branch 'origin'	2020-11-23 21:34:08 +01:00
Emelie Nilsso	2ea06ffab8	Modified uppmax and ampliseq specific config to fit with the divided preparation of the database	2020-11-23 21:20:36 +01:00
Thiseas C. Lamnidis	71d1ff2226	Add params block to sdag queue ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2020-11-18 13:04:46 +01:00
Thiseas C. Lamnidis	da781907f2	Move sdag queue specification block in sdag profile	2020-11-17 19:45:06 +01:00
Maxime Borry	c95fd9d52f	Merge pull request #186 from jfy133/shh-singularity-runoptions ... Remove custom singularity runOptions from SHH config	2020-11-10 15:39:40 +01:00
James A. Fellows Yates	9d4d682867	Update shh.config	2020-11-10 15:14:03 +01:00
Gisela Gabernet Garriga	885f0ce5f6	awsbatch config update	2020-11-09 22:41:38 +01:00
lecorguille	90d1f9072b	Add ABiMS - autoMounts = false	2020-10-22 18:18:55 +02:00
lecorguille	a63ca751ee	Add ABiMS	2020-10-22 16:57:41 +02:00
James A. Fellows Yates	804f53c58c	Merge pull request #178 from jfy133/master ... Add Max Planck Computing and Data Facility Cobra/Raven Clusters	2020-10-22 13:34:11 +02:00
James A. Fellows Yates	3995057d7f	Update mpcdf.config	2020-10-22 10:42:46 +02:00
James A. Fellows Yates	05deeca2d6	Update mpcdf.config	2020-10-15 14:22:35 +02:00
James A. Fellows Yates	e26c22b2f1	Update shh.config	2020-09-29 14:03:35 +02:00
MaxUlysse	2ccbdd3367	update params to latest version	2020-09-28 13:59:42 +02:00
MaxUlysse	8c0cc4b9ec	code polishing	2020-09-25 09:57:50 +02:00
MaxUlysse	81f910cc95	add specific BamQC config	2020-09-25 09:49:43 +02:00
MaxUlysse	fbe7bd133a	update uppmax specific sarek config	2020-09-25 08:33:53 +02:00
James A. Fellows Yates	11f1fb71db	Update mpcdf.config	2020-09-16 10:21:58 +02:00
James A. Fellows Yates	bbbdd3cb0f	Update mpcdf.config	2020-09-16 10:21:42 +02:00
James A. Fellows Yates	5b3492d240	Update mpcdf.config	2020-09-16 10:21:26 +02:00
James A. Fellows Yates	3115963b3e	Update mpcdf.config	2020-09-15 19:53:27 +02:00
James A. Fellows Yates	c6f7573d01	Update mpcdf.config	2020-09-15 17:48:54 +02:00
James A. Fellows Yates	bf87ec24e7	Update mpcdf.config	2020-09-15 17:45:38 +02:00
Edmund Miller	2c06019d89	fix(utd): Add check for less than 12 cpu	2020-09-13 20:46:14 -05:00
Edmund Miller	dc2735207e	feat(utd): add Kim queue	2020-09-13 20:46:10 -05:00
James A. Fellows Yates	3b7902d11b	Mad multi-core increase CPUs on retry	2020-09-06 08:23:35 +02:00
James A. Fellows Yates	4335e5deb7	Update mpcdf.config	2020-09-04 20:17:09 +02:00
James A. Fellows Yates	b4e275c3b9	Add MPCDF for EAGER	2020-09-04 19:57:25 +02:00
James A. Fellows Yates	5c7ab234b6	Create mpcdf.config	2020-09-04 19:55:40 +02:00
James A. Fellows Yates	0a685c1cc2	Update mpcdf.config	2020-09-03 20:24:11 +02:00
James A. Fellows Yates	42a1a15970	Create mpcdf.config	2020-09-03 20:11:56 +02:00
James A. Fellows Yates	c3fa87e4bc	Add microbiome screening profile for NT sized MALT runs for nf-core/eager@SHH	2020-08-11 09:18:36 +02:00
drpatelh	b804076959	Remove hard Singularity version	2020-08-03 11:38:10 +01:00
maxibor	69a0bd572b	add temporary CDAG setting for SHH config	2020-07-23 15:38:28 +02:00
James A. Fellows Yates	d38ffc289b	Merge pull request #173 from jfy133/shh-eager-hops-update ... Remove now deprecated EAGER flag for HOPS profile	2020-07-20 11:34:49 +02:00
James A. Fellows Yates	57ac9257a9	Remove now deprecated EAGER flag for HOPS profile	2020-07-20 11:29:12 +02:00
Alexander Peltzer	a498e98342	Merge pull request #170 from jfy133/master ... Make walltimes more sophisticated and add a HOPS profile for nf-core/eager @ SHH	2020-07-15 15:11:24 +02:00
James A. Fellows Yates	84e03b8264	Re-bump default walltimes after debugging/testing	2020-07-11 18:31:04 +02:00
James A. Fellows Yates	8f6409d144	Remove min support percent value to avoid confusion	2020-07-08 15:26:19 +02:00
James A. Fellows Yates	1af9ce293c	Update hops profile based on requests from pathogen group	2020-07-08 15:22:33 +02:00
James A. Fellows Yates	c57a404f18	Add desc for hops	2020-07-08 10:45:43 +02:00
jfy133	15dad7e2e7	Add caveats for EAGER @ SHH profiles	2020-07-08 09:47:03 +02:00
jfy133	926c14f7ee	Cleverer process time submission	2020-07-08 09:36:56 +02:00
jfy133	563c27e1bb	Try again to get better time resource submission	2020-07-08 09:36:28 +02:00
James A. Fellows Yates	c6905b609e	Update shh.config	2020-07-08 09:25:21 +02:00
James A. Fellows Yates	b360ce26bc	Update shh.config	2020-07-08 09:24:06 +02:00
James A. Fellows Yates	31edb4b5d7	Update shh.config	2020-07-08 09:20:00 +02:00
James A. Fellows Yates	aac3478e86	Add better task time values to account for large data	2020-07-08 09:12:11 +02:00
James A. Fellows Yates	737d826932	Update shh.config	2020-07-08 08:36:04 +02:00
piotr-faba-ardigen	ba24f1a1c8	Merge pull request #168 from piotr-faba-ardigen/add_bi_config ... Fix bi config	2020-07-07 14:56:43 +02:00
James A. Fellows Yates	fcdbeaa446	Merge branch 'master' into master	2020-07-07 14:34:10 +02:00
James A. Fellows Yates	af01fccba1	Add a HOPS profile for nf-core/eager @ SHH	2020-07-07 14:31:11 +02:00
Piotr Faba	cb7a6f756a	reduce complexity	2020-07-07 13:48:28 +02:00
James A. Fellows Yates	5517d2cbe0	Remove default non-profile bwa parameters from eager profile ... I realised today this is dangerous as these would not necessarily be reported if a user doesn't understand the profiles. Therefore removing these so nf-core/eager defaults are always used unless a specific profile (which would be described in the command itself) is explicitly named.	2020-07-07 13:29:13 +02:00
Piotr Faba	4181184f58	fix spaces	2020-07-02 22:00:37 +02:00
Piotr Faba	4828e78708	fix error introduced earlier	2020-07-02 21:57:44 +02:00
James A. Fellows Yates	530da4d8c0	Merge pull request #167 from jfy133/master ... Bump number of eager @shh retries to account for deep sequencing data	2020-06-30 11:33:29 +02:00
James A. Fellows Yates	c52428cd72	Bump number of eager @shh retries to account for deep sequencing data	2020-06-30 08:19:25 +02:00
Adrian	e375ad97ad	reverting autoMounts due to bug	2020-06-26 13:39:37 +01:00
Phil Ewels	cd9fbb22dc	Merge pull request #161 from ewels/uct_hpc ... Update UCT hex -> hpc	2020-06-22 09:18:43 +02:00
Alexander Peltzer	7774a6a8f3	Merge pull request #163 from piotr-faba-ardigen/add_bi_config ... resolve #162 bug	2020-06-19 08:57:44 +02:00
Piotr Faba	cb26bef3f3	resolve #162 bug	2020-06-18 20:30:05 +02:00
Phil Ewels	53e118210f	Copy over HPC config	2020-06-17 15:20:22 +02:00
Phil Ewels	dbfcd7c5e9	Rename uct_hex > uct_hpc	2020-06-17 15:17:22 +02:00
Phil Ewels	17824d2d62	Merge czbiohub_aws_highpriority profile into czbiohub_aws	2020-06-16 15:20:39 +02:00
phue	6d356cc918	CBE: don't load singularity module ... singularity is now installed from CentOS repos, the environment module will be removed	2020-06-05 12:07:26 +02:00
Alexander Peltzer	f877644059	Merge branch 'master' into master	2020-05-29 11:43:47 +02:00
Alexander Peltzer	32ec230098	Merge pull request #156 from piotr-faba-ardigen/add_bi_config ... Add bi config	2020-05-27 21:03:15 +02:00
Piotr Faba	f139750bf4	print the error message before throwing Exception	2020-05-27 19:14:43 +02:00
Piotr Faba	3c695ba71c	test error display	2020-05-27 18:00:47 +02:00
Alexander Peltzer	6011419454	Merge pull request #154 from jfy133/master ... Update SHH nf-core/eager group-specific profiles	2020-05-27 17:52:09 +02:00
Piotr Faba	18d8edb046	add description and profile	2020-05-27 17:41:19 +02:00
Piotr Faba	66f191a1cf	declate NXF_GLOBAL_CONFIG in ci	2020-05-27 16:30:00 +02:00
Piotr Faba	2685275952	switch include off	2020-05-27 16:24:47 +02:00
Piotr Faba	c31b03108c	retry without Exception	2020-05-27 16:22:56 +02:00
Piotr Faba	1354ae4063	add bi config	2020-05-27 16:19:15 +02:00
James A. Fellows Yates	d070ed70d1	Update BWA settings based on feedback	2020-05-26 11:11:42 +02:00
James A. Fellows Yates	e31e781f29	Remove debugging	2020-05-26 11:07:06 +02:00
Harshil Patel	5981e5ec27	Merge pull request #153 from FriederikeHanssen/cfc_scratch ... Add scratch = true to avoid writing of intermediate file to /tmp	2020-05-22 15:48:00 +01:00
James A. Fellows Yates	ff915ee504	Update shh.config	2020-05-12 12:47:59 +02:00
James A. Fellows Yates	8225e07819	Condensed base params and added names for debugging	2020-05-12 12:47:25 +02:00
James A. Fellows Yates	4814bac1c3	Fix sub-profiles	2020-05-12 12:42:42 +02:00
James A. Fellows Yates	38e9e54932	Merge pull request #151 from jfy133/master ... Add additional custom nf-core/eager params for SHH profile	2020-05-07 09:25:02 +02:00
James A. Fellows Yates	cf6e697f0b	Further update aln based on modifications of EAGER defaults	2020-05-07 09:16:08 +02:00
James A. Fellows Yates	d42d7f4146	Sets the bwa aln parameter to 0.01 which is more commonly used at SHH	2020-05-04 21:02:16 +02:00
FriederikeHanssen	d6813d9c39	Add scratch = true to avoid writing of intermediate file to /tmp	2020-05-04 17:09:43 +02:00
MaxUlysse	e6f4d58fa6	update rnafusion munin specific config	2020-04-28 17:06:04 +02:00
Adrian	ad12bd4ad1	testing automounts	2020-04-28 16:03:06 +01:00
Harshil Patel	2300d5a962	Update genomes.config	2020-04-09 18:22:41 +01:00
MaxUlysse	50a44d037b	better docs and organisation of giles	2020-04-09 17:02:36 +02:00
Maxime Garcia	34dc18faf6	Update uppmax.config	2020-04-09 11:35:37 +02:00
Adrian Larkeryd	405801638a	icr_davros sarek config description	2020-04-08 11:56:17 +01:00
Adrian Larkeryd	78be4b358e	icr_davros igenomes base	2020-04-08 11:55:16 +01:00
Maxime Garcia	d1ff87a416	Merge pull request #145 from bioatlas/master ... Adding UPPMAX specific config for ampliseq	2020-03-31 15:46:21 +02:00
Daniel Lundin	c8de9be701	Adding UPPMAX specific config for ampliseq	2020-03-31 15:17:24 +02:00
MaxUlysse	db2dd4458b	Merge remote-tracking branch 'upstream/master' into UPPMAX	2020-03-30 16:41:08 +02:00
MaxUlysse	8b570507cd	update s	2020-03-30 16:40:11 +02:00
ggabernet	c81f693f73	add cfc_dev config	2020-03-23 17:16:34 +01:00
Olga Botvinnik	52369ba6ad	Add AaegL5.0 config	2020-03-17 16:45:20 -07:00
Maxime Garcia	123132d89a	Update munin.config ... fix typo	2020-03-12 17:23:55 +01:00
Phil Ewels	5a3bdcca5b	Merge pull request #139 from Emiller88/utd ... fix(ganymede): use singularity/2.4.5	2020-03-11 16:54:01 +00:00
Maxime Garcia	b6d52fdb89	Update conf/pipeline/sarek/munin.config	2020-03-11 15:48:29 +01:00
Maxime Garcia	0f34d757a9	Update munin.config	2020-03-11 15:48:17 +01:00
MaxUlysse	d24a296a01	add munin/rnafusion specific config	2020-03-11 14:02:01 +01:00
MaxUlysse	dd1ddf864b	update sarek munin config	2020-03-11 14:01:28 +01:00
Edmund Miller	cece853663	fix(ganymede): use singularity/2.4.5 ... Our 3.2.1 doesn't work right with snakemake or nextflow	2020-03-10 21:03:24 -05:00
Edmund Miller	c42bb07981	fix: Singularity => singularity ... For some reason ours are lowercase	2020-03-10 09:55:17 -05:00
Edmund Miller	123c44c56d	feat: add initial ganymede config	2020-03-09 16:18:41 -05:00
marcel-keller	8e3803e4d7	Update ebc.config	2020-03-09 16:57:45 +02:00
marcel-keller	c00bbe982b	Update ebc.config	2020-03-09 16:51:38 +02:00
marcel-keller	3b57519500	Update ebc.config	2020-03-09 16:48:50 +02:00
marcel-keller	de914e56ee	Create ebc.config	2020-03-09 16:08:01 +02:00
Evan Floden	d8ad376f71	Merge branch 'master' into master	2020-03-06 10:29:50 +00:00
Alexander Peltzer	59a787b179	Merge pull request #122 from marchoeppner/ccga-config ... Removing old CCGA profile from docs and linting	2020-03-06 11:17:08 +01:00
mseybold	52842de88b	Update cfc.config ... test failed, so added the the default queue	2020-03-06 10:46:37 +01:00
mseybold	8e42bbd7d0	Update cfc.config ... We just added some new HighMem nodes to the cfc, Partition/queue name is qbic, each node has 128Cores and 2TB of RAM. The old queue (Name compute) is set to default by slurm. Each process over 60GB of RAM or over 20cpus should run on those new nodes. So added the queue State and adjusted the max_memory and max_cpu setting.	2020-03-06 10:25:08 +01:00
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