490 commits

Author	SHA1	Message	Date
kpj	e1b2fd6085	Fix bug in Snakemake file regex	2020-09-11 13:49:05 +02:00
kpj	ec0577ae5b	Add Snakemake to language array	2020-09-11 13:31:57 +02:00
NicolasVuillamy	c86e90b3d0	Solve conflicts + format	2020-09-09 20:22:32 +02:00
NicolasVuillamy	f072bc5c8d	Merge remote-tracking branch 'github/master'	2020-09-09 20:18:21 +02:00
Marco Ferrari	83666ffaba	Fix getting filename for hidden files	2020-09-08 19:20:49 +02:00
Lucas Gravley	a6c9656015	fixing vars	2020-09-08 09:47:57 -05:00
kpj	6f6e6e9d03	[Snakemake] Remove wrong function argument	2020-09-08 11:26:48 +02:00
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	ad262196ba	[Snakemake] Also lint 'Snakefile' (without '.smk' suffix)	2020-09-08 09:11:54 +02:00
kpj	53f551c8b0	[Snakemake] Add '--config' parameter to 'snakefmt' calls	2020-09-07 17:26:58 +02:00
kpj	1e453be7fa	[Snakemake] Update codebase	2020-09-07 16:49:07 +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	c58bab2627	Merge pull request #677 from v1v/feature/version ... Print version, date and revision	2020-09-04 10:35:38 -05:00
Lucas Gravley	b29eb851d3	make pretty	2020-09-04 10:14:47 -05:00
Lukas Gravley	a3fcb3ea7c	Merge pull request #675 from dmerrick/honoring-disable-errors ... Making MULTI_STATUS honor DISABLE_ERRORS setting	2020-09-04 09:15:06 -05:00
Lukas Gravley	eb36fb7d7c	Merge branch 'master' into master	2020-09-04 08:53:34 -05:00
NicolasVuillamy	21d75fb89e	Groovy traps .nf extension (nextflow) + upgrade npm-groovy-lint	2020-09-04 11:54:31 +02:00
Victor Martinez	d3c992bec7	Print version, date and revision	2020-09-04 09:09:20 +01:00
Dana Merrick	c64c5c8d60	Cleaner solution	2020-09-03 19:37:10 -04:00
Dana Merrick	dd84550d46	Honoring DISABLE_ERRORS	2020-09-03 19:23:24 -04:00
Lucas Gravley	c4bbf03935	fixing debug	2020-09-03 10:12:29 -05:00
Lucas Gravley	d78e707cba	no source needed	2020-09-03 09:57:20 -05:00
Lucas Gravley	8a51e59be7	even easier	2020-09-03 09:20:00 -05:00
Lucas Gravley	72fd3e3b87	super simple	2020-09-03 09:12:49 -05:00
Lucas Gravley	f5e39e5aad	fix typo and add check	2020-09-02 09:26:01 -05:00
Josselin	f34b084586	Add support for black config file	2020-09-02 11:28:57 +02:00
Marco Ferrari	de4b8a4fa0	Add shfmt and fixes back	2020-09-01 00:06:15 +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	f5331bdcd3	Skip shfmt if no .editorconfig file is present	2020-08-31 19:30:50 +02:00
Marco Ferrari	f90c3a289b	Check if report output folder exists before listing	2020-08-31 19:22:50 +02:00
Marco Ferrari	b3a980e06f	Fix bash-exec and terrascan versions	2020-08-31 19:22:49 +02:00
Marco Ferrari	0d849cd5e0	Lint shell files with shfmt	2020-08-31 19:22:49 +02:00
Lucas Gravley	a32d0c1314	here	2020-08-28 14:08:08 -05:00
Lucas Gravley	b7781ba295	forgot quote	2020-08-28 11:54:31 -05:00
Lucas Gravley	9be83e0166	merge master	2020-08-28 11:46:11 -05:00
Lucas Gravley	345a6626e7	put it back	2020-08-28 11:42:14 -05:00
Lukas Gravley	10f44786ce	Merge pull request #641 from github/isExec ... adding bash-exec	2020-08-28 10:37:43 -05:00
Lucas Gravley	40fddbad79	get name even	2020-08-28 10:12:02 -05:00
Lucas Gravley	0404c39203	adding exec	2020-08-28 09:56:53 -05:00
Lucas Gravley	d9f35b2af7	more cleanupo	2020-08-27 14:26:05 -05:00
Lucas Gravley	4bf0aee923	Make it happy	2020-08-27 14:12:24 -05:00
Lucas Gravley	94e03d50ac	better loop	2020-08-27 14:01:43 -05:00
Lucas Gravley	9cae4c7f6d	better	2020-08-27 09:00:54 -05:00
Cesar Rodriguez	815f8236dd	Updates scan command for Terrascan	2020-08-26 22:53:00 -04:00
Cesar Rodriguez	e060679ea8	Updates terrascan command	2020-08-26 22:53:00 -04:00
Eddy Nakamura	9c44d2d503	changing command - 2	2020-08-26 11:58:28 -03:00
Eddy Nakamura	b83e4c99ed	updating command	2020-08-26 11:42:05 -03:00
Lucas Gravley	454fa09b81	Fixed it?	2020-08-26 08:50:53 -05:00