629 commits

Author	SHA1	Message	Date
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
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
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	a3c8b22e2c	fix duplicate names	2020-09-03 09:56:34 -05:00
Lucas Gravley	6ac933dc8c	fix print	2020-09-03 09:34:39 -05:00
Lucas Gravley	165b29cbe1	fix array	2020-09-03 09:21:22 -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
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	f5e39e5aad	fix typo and add check	2020-09-02 09:26:01 -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	de4b8a4fa0	Add shfmt and fixes back	2020-09-01 00:06:15 +02:00