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Author	SHA1	Message	Date
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
Alexander Peltzer	2801f25657	Merge pull request #166 from adrlar/master ... Fixing an autoMounts bug for icr_davros	2020-06-26 17:52:05 +02:00
Adrian	5b890d571a	adding icr_davros to list	2020-06-26 13:40:15 +01:00
Adrian	e375ad97ad	reverting autoMounts due to bug	2020-06-26 13:39:37 +01:00
Phil Ewels	a7c8cbc410	Fix new CI test	2020-06-26 14:30:53 +02:00
Phil Ewels	b587a2d031	Remove env vars from CI test and try running -show-profiles	2020-06-26 14:24:51 +02:00
Phil Ewels	28027a8489	Prince config - use function to check if env SCRATCH is set	2020-06-26 14:22:32 +02:00
Phil Ewels	da46b1cd9a	Remove --custom_config_base from CI test command	2020-06-26 14:13:49 +02:00
Phil Ewels	824d9b86bc	Set params.custom_config_base in nextflow.config	2020-06-26 14:08:24 +02:00
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
Alexander Peltzer	bb7f67e2b5	Merge pull request #160 from ewels/master ... Merge czbiohub_aws_highpriority profile into czbiohub_aws	2020-06-17 19:20:07 +02:00
Phil Ewels	18a1a319ec	More uct_hex references	2020-06-17 15:25:07 +02:00
Phil Ewels	29f5fa6ce4	uct_hpc docs, readme	2020-06-17 15:22:42 +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
Phil Ewels	e091ec259e	Merge pull request #158 from phue/singularity_global ... CBE: don't load singularity module	2020-06-05 12:20:39 +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	adf90f3994	Merge pull request #146 from adrlar/master ... Adding config for ICR davros cluster	2020-06-03 20:09:49 +02:00
Adrian	3e4db8c845	adding icr_davros to test	2020-06-03 14:55:58 +01:00
Alexander Peltzer	f877644059	Merge branch 'master' into master	2020-05-29 11:43:47 +02:00
Alexander Peltzer	0d5899eb26	Merge pull request #157 from nf-core/bi-docs ... Add BI to main readme.md	2020-05-28 10:25:19 +02:00
Alexander Peltzer	dd56355c7c	Update bi.md ... No trailing spaces it said.	2020-05-28 10:18:16 +02:00
Alexander Peltzer	f4df5b5a75	Add BI Docs	2020-05-28 10:16:22 +02:00
Alexander Peltzer	0efa9f248e	Add BI to main readme.md	2020-05-28 10:12:50 +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
Alexander Peltzer	27f3207cb9	Merge pull request #155 from piotr-faba-ardigen/add_bi_config ... Add BI internal config	2020-05-27 17:49:41 +02:00
Piotr Faba	18d8edb046	add description and profile	2020-05-27 17:41:19 +02:00
Piotr Faba	f5e2a9f9f3	try without dummy.config: use relative path	2020-05-27 16:55:37 +02:00
Piotr Faba	3ad0003979	test without dummy config	2020-05-27 16:46:08 +02:00
Piotr Faba	1a9db371c3	remove echos	2020-05-27 16:43:32 +02:00
Piotr Faba	ac47d020cb	debug: continue	2020-05-27 16:38:11 +02:00
Piotr Faba	ff5fdd097b	debug	2020-05-27 16:35:55 +02:00
Piotr Faba	ab3070582e	Fix paths to dummy.config	2020-05-27 16:32:19 +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	0943ba088a	Mention SHH EAGER group-specific profiles	2020-05-26 11:14:42 +02:00
James A. Fellows Yates	d070ed70d1	Update BWA settings based on feedback	2020-05-26 11:11:42 +02:00