295 commits

Author	SHA1	Message	Date
James A. Fellows Yates	737d826932	Update shh.config	2020-07-08 08:36:04 +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
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
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