192 commits

Author	SHA1	Message	Date
Lucas Gravley	8be7c6df85	remove cache folder	2020-10-13 14:17:40 -05:00
Tim Jones	a8746a7159	Add support for Terragrunt files	2020-10-08 18:18:22 +02:00
Marco Ferrari	68e15659b8	Centralize file list building logic in buildFileList.sh	2020-10-07 16:36:49 +02:00
Marco Ferrari	973bfdea8e	Initialize all log-related ASAP	2020-09-29 22:46:24 +02:00
Lukas Gravley	84c79a186b	Merge branch 'master' into master	2020-09-22 08:56:09 -05:00
Marco Ferrari	f24f52be11	Lint with Kubeval and fixes	2020-09-22 01:49:01 +02:00
Marco Ferrari	6168112f61	Fix ERROR_ON_MISSING_EXEC_BIT initialization	2020-09-21 14:43:44 +02:00
kpj	6f6004275f	In anticipation of snakefmt 0.1.6, start using --check and --compact-diff	2020-09-18 16:32:01 +02:00
Marco Ferrari	5cefb9209f	Make bash-exec errors or warnings configurable	2020-09-15 22:40:12 +02:00
NicolasVuillamy	e470df5431	Fix file filters: Reorder arguments to LintCodeBase function	2020-09-15 08:15:53 +02:00
Lukas Gravley	79b055babe	Merge pull request #707 from ferrarimarco/fix-node-modules ... Fix list files function typos	2020-09-10 11:21:54 -05:00
Lucas Gravley	b232c5b970	this is the way./..	2020-09-10 10:34:04 -05:00
Marco Ferrari	ad9c0081f4	Fix list files function typos	2020-09-10 12:10:12 +02:00
NicolasVuillamy	27afc50d60	Set GROOVY Linter failure level to warning	2020-09-10 11:07:05 +02:00
NicolasVuillamy	f072bc5c8d	Merge remote-tracking branch 'github/master'	2020-09-09 20:18:21 +02:00
Lucas Gravley	b5d42bf181	this makes no sense	2020-09-09 10:37:02 -05:00
Lucas Gravley	880380d118	if i could only read	2020-09-09 10:18:12 -05:00
Lucas Gravley	dbd4cd673d	this has to be right	2020-09-09 10:04:21 -05:00
Lucas Gravley	eb67d9b9c6	fix that dumb action	2020-09-09 09:28:39 -05:00
Lucas Gravley	bae75b456b	more fix	2020-09-09 09:24:57 -05:00
Lucas Gravley	17c3ded695	i forgot how this works	2020-09-09 09:24:27 -05:00
Lukas Gravley	e9811c85d6	Update lib/worker.sh ... yes Co-authored-by: Goryudyuma(Kei.Matsumoto) <6211370+Goryudyuma@users.noreply.github.com>	2020-09-08 16:00:12 -05:00
Lucas Gravley	fd42f4b3fb	science...	2020-09-08 15:45:17 -05:00
Lucas Gravley	0e5f996c3c	look at folders and not file names	2020-09-08 12:16:59 -05:00
Lucas Gravley	a0d4012b67	like this?	2020-09-08 12:01:17 -05:00
Lucas Gravley	53995952e0	Merge branch 'master' into just-filter-the-git-folder	2020-09-08 10:43:59 -05:00
kpj	581f07a32b	[Snakemake] Fix 'LINTER_NAME'	2020-09-08 10:19:56 +02:00
kpj	8ac1c99a2e	[Snakemake] Support both formatting using 'snakefmt' and linting using 'snakemake --lint'	2020-09-08 09:38:48 +02:00
kpj	53f551c8b0	[Snakemake] Add '--config' parameter to 'snakefmt' calls	2020-09-07 17:26:58 +02:00
kpj	0c5029bf67	[Snakemake] Actually run 'snakefmt' tests	2020-09-07 17:20:56 +02:00
NicolasVuillamy	04c93b4ff5	Add management of FILTER_REGEX_INCLUDE and FILTER_REGEX_EXCLUDE options	2020-09-05 12:25:44 +02:00
Lukas Gravley	828de134a9	this should be right	2020-09-04 13:22:01 -05:00
Goryudyuma(Kei.Matsumoto)	b31b696e00	Just filter the .git folder	2020-09-05 03:08:26 +09:00
NicolasVuillamy	21d75fb89e	Groovy traps .nf extension (nextflow) + upgrade npm-groovy-lint	2020-09-04 11:54:31 +02:00
Lukas Gravley	b012d72952	Merge pull request #662 from montyly/dev-black-config-file ... Add support for black config file	2020-09-02 09:57:44 -05:00
Lucas Gravley	a756e40157	typo	2020-09-02 09:07:39 -05:00
Lucas Gravley	6040030c8a	Adding more paths to ignore	2020-09-02 09:05:36 -05:00
Josselin	f34b084586	Add support for black config file	2020-09-02 11:28:57 +02:00
Marco Ferrari	30763f2575	Streamline shell file list building	2020-08-31 23:47:48 +02:00
Lucas Gravley	98c2eec42a	small clean	2020-08-31 14:34:14 -05:00
Marco Ferrari	228a86e5c0	Remove duplicate output lines when checking for ZSH scripts	2020-08-31 19:56:49 +02:00
Marco Ferrari	798311822a	Add file path to ZSH warning messages	2020-08-31 19:47:05 +02:00
Marco Ferrari	833dcb8bd8	Don't check zsh files with shfmt	2020-08-31 19:31:22 +02:00
Marco Ferrari	644e69131b	Fix shfmt test	2020-08-31 19:22:50 +02:00
Marco Ferrari	0d849cd5e0	Lint shell files with shfmt	2020-08-31 19:22:49 +02:00
Lucas Gravley	13e87dd021	lots of cleanup	2020-08-31 11:51:03 -05:00
Lucas Gravley	958f70fe67	its real picky	2020-08-31 10:11:12 -05:00
Lucas Gravley	a32d0c1314	here	2020-08-28 14:08:08 -05:00
Lucas Gravley	a9bc2068f7	they come in pairs	2020-08-28 13:50:23 -05:00
Lucas Gravley	633418aa8a	fix var	2020-08-28 13:47:15 -05:00