317 commits

Author	SHA1	Message	Date
Edmund Miller	dc2735207e	feat(utd): add Kim queue	2020-09-13 20:46:10 -05:00
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