645 commits

Author	SHA1	Message	Date
Marco Ferrari	d43fcdc666	Sort environment variables when printing debug info	2020-09-26 00:51:53 +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
Lukas Gravley	f290145dfa	Update linter.sh	2020-09-21 13:51:46 -05:00
Lukas Gravley	06cb2ebb6f	Update linter.sh	2020-09-21 13:50:58 -05:00
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
kpj	5b51c2bd92	Use '--compact-diff' instead of '--diff' for snakefmt	2020-09-14 09:36:33 +02:00
Joseph Marino	2698bdfbc3	Fixed a typo in code comments ... Replaced the term "CSS" with "HTML" in code comments for the HTML_LINTER_RULES variable.	2020-09-11 15:16:55 -04:00
kpj	11f437df4c	Fix usage of FILE_ARRAY_SNAKEMAKE	2020-09-11 13:51:15 +02:00
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
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
Lucas Gravley	f432ef2116	fix spaces	2020-09-10 10:25:56 -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	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
Lukas Gravley	9f3eb7d454	Merge pull request #679 from Goryudyuma/just-filter-the-git-folder ... Just filter the .git folder	2020-09-09 10:53:19 -05:00
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
Marco Ferrari	83666ffaba	Fix getting filename for hidden files	2020-09-08 19:20:49 +02:00
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
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	0c5029bf67	[Snakemake] Actually run 'snakefmt' tests	2020-09-07 17:20:56 +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	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
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