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Author SHA1 Message Date
dependabot[bot]
eef7b50ea3
Bump snakemake from 6.8.0 to 6.8.1 in /dependencies (#2004) 
* Bump snakemake from 6.8.0 to 6.8.1 in /dependencies

Bumps [snakemake](https://github.com/snakemake/snakemake) from 6.8.0 to 6.8.1.
- [Release notes](https://github.com/snakemake/snakemake/releases)
- [Commits](https://github.com/snakemake/snakemake/compare/v6.8.0...v6.8.1)

---
updated-dependencies:
- dependency-name: snakemake
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* fixed dead var

* typo in name

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Lukas Gravley <admiralawkbar@github.com>
 2021-09-27 11:02:18 -05:00
Masaya Suzuki
0e1a1e50d6
Add Gitleaks for secret scanning (#1951) 
* Add actionlint

* adding gitleaks

* rm secretlint

* Update .gitleaks.toml

Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
 2021-09-27 09:32:18 -05:00
Lukas Gravley
a3cce70fa3
adding composer code (#1950) 
* adding composer code

* making it better

* adding composer bin

* adding some logic

* make shellfmt happy
 2021-09-10 09:43:20 -05:00
Lukas Gravley
c649496209
suppress warn messages (#1943) 2021-09-07 10:12:49 -05:00
JonZeolla
d90f45a3cc
Install type stubs at mypy runtime (#1937) 2021-09-07 08:56:30 -05:00
Kurt von Laven
8227f79074
Add a template config file for ShellCheck (#1900) 
* Improve wording of LINTER_RULES_PATH docs (#1634).

* Add a template config file for ShellCheck (#1633).

Instruct ShellCheck to search SCRIPTDIR, the directory that the script
being linted is in, for other scripts that are sourced. Otherwise, the
commonly-used source command results in linter error SC1091. See
https://github.com/koalaman/shellcheck/wiki/SC1091 for more details.

* fix line ending

Co-authored-by: Lukas Gravley <admiralawkbar@github.com>
 2021-08-30 11:19:56 -05:00
Lukas Gravley
5f65429f2c
adding tflint (#1899) 
* adding tflint

* fixed array

* i thought this was fixed
 2021-08-30 09:47:50 -05:00
Lukas Gravley
148622b273
Sqlfluff (#1834) 
* adding sqlfluff

* adding sqlfluff

* update test

* adding sql file array
 2021-08-05 15:32:27 -05:00
Lukas Gravley
ab24b82199
Adding actionlint (#1775) 
* Adding action lint

* adding tests

* adding tests

* Update Dockerfile

Co-authored-by: Masaya Suzuki <15100604+massongit@users.noreply.github.com>

* cleanup name

* fix test

* typo

* fix file name

* fix our own errors

* more cleanup

* angry

* make it happy

* stop double jobs

Co-authored-by: Masaya Suzuki <15100604+massongit@users.noreply.github.com>
 2021-07-19 09:28:49 -05:00
Lukas Gravley
1481793072
adding clang (#1762) 
* adding clang

* fix hado

* adding files

* fixing naming

* fixing test

* fixing space

* removing config file

* fix tests

* fix tests

* fix file array
 2021-07-14 14:43:10 -05:00
Aldana Vaca
8b75fbf345
Adding terrascan config file (#1761) 
* adding terrascan config file

* fix line ending

Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
 2021-07-14 10:20:24 -05:00
Thomas Iguchi
fad8d1cde2
Added support for changing Checkstyle rules file name (#1760) 
Resolves https://github.com/github/super-linter/issues/680
 2021-07-14 09:45:07 -05:00
Lukas Gravley
b3e0c02dc5
yamllint format (#1754) 
* standard

* parsable
 2021-07-13 11:04:58 -05:00
Lukas Gravley
100c674c6d
adding tflint config (#1753) 2021-07-13 09:44:27 -05:00
Lukas Gravley
d24eb27b4c
move from jsonlint to eslint (#1752) 
* move from jsonlint to eslint

* move from jsonlint to eslint

* adding test
 2021-07-13 09:10:37 -05:00
Stepan Koltsov
e059100991
Ignore files marked with @generated marker (#1689) 
* Ignore files marked with @generated marker

`@generated` marker is used by certain tools to understand that the
file is generated, so it should be treated differently than a file
written by a human:
* these files do not need to be reformatted,
* diffs in these files are less important,
* and linters should not be invoked on these files.

This PR proposes builtin support for `@generated` marker (and
`@not-generated` marker to mark file as not generated when it
contains `@generated` marker, like `README.md`).

I have not found a standard for a generated file marker, but:
* Facebook [uses `@generated` marker](https://tinyurl.com/fb-generated)
* Phabricator tool which was spawned from Facebook internal tool
  [also understands `@generated` marker](https://git.io/JnVHa)
* Cargo inserts `@generated` marker into [generated Cargo.lock files](https://git.io/JnVHP)

Super-linter supports regex includes and excludes, but they are
harder to maintain (each repository needs to be configured) than
patching the tools which generate the files.

My personal story is that I maintain rust-protobuf crate, which
started emitting `@generated` markers [six years ago](https://git.io/JnV5h)
after a request of a Phabricator user.

Test Plan:

Create a test file `test.sh`:

```
echo $a
```

Run:

```
docker run -e RUN_LOCAL=true -v $HOME/tmp/g:/tmp/lint super-linter-test
```

Result is:

```
In /tmp/lint/test.sh line 1:
echo $a
^-- SC2148: Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive.
     ^-- SC2154: a is referenced but not assigned.
     ^-- SC2086: Double quote to prevent globbing and word splitting.
...
2021-06-22 23:46:16 [ERROR]   ERRORS FOUND in BASH:[1]
```

Now add `@generated` to the file and run again:

```
2021-06-22 23:47:13 [NOTICE]   All file(s) linted successfully with no errors detected
```

Additionally, add `@not-generated` in addition to `@generated`, and
linter error pops up again.

* cleanup

* remove space

* fix non utf return

* fix non utf return

Co-authored-by: Lukas Gravley <admiralawkbar@github.com>
 2021-06-28 07:59:11 -05:00
Lukas Gravley
c4280ea4e1
LINTER_RULE_PATH fix (#1649) 
* adding root code

* removbe a typio
 2021-06-10 13:09:24 -05:00
Lukas Gravley
2c135d4a17
adding rules file (#1644) 
* adding rules file

* fix naming

* cleanup

* make smart

* fixing the make

* adding template

* white space

* not sure how i got windows

* found the space
 2021-06-09 11:53:11 -05:00
Lukas Gravley
4faa6433ab
adding find algorithm (#1640) 
* adding find

* add default value
 2021-06-08 10:40:59 -05:00
Lukas Gravley
6ce478c991
Kube (#1609) 
* adding var

* adding var

* bug

* spacing

* better name
 2021-06-01 15:04:25 -05:00
Lukas Gravley
83badbc49c
Image 4.0 (#1565) 
* adding new one...

* adding automation

* linter

* pull apart for faster builds

* maybe

* update automation

* fix that

* prime is smart

* fixed it

* quotes

* fix build image

* inpec

* typo

* forgot backslash

* fixed hairbrain logic

* this should help cleanup

* i hate r

* order

* maybe fix r

* maybe fix r

* update readme

* remove spaces

* update
 2021-05-25 10:14:43 -05:00
Lukas Gravley
3e0bd7fff4
Eslint for json jsonc and json5 (#1524) 
* adding it

* fix typo

* fix tests

* adding back jsonlint

* adding back jsonlint

* fix spacing

* found the typo

* add tests

* adding rules for json

* add to local
 2021-05-11 10:54:58 -05:00
Lukas Gravley
5d96acadf1
remove more dead weight (#1530) 
* remove more dead weight

* more cleaner

* falling into place

* tie dotnet to version

* new low
 2021-05-10 09:58:30 -05:00
Lukas Gravley
5d2ea81f00
Cpp (#1492) 
* adding cpp

* adding cpp

* tests

* make test better

* fix test
 2021-05-04 13:24:41 -05:00
Lukas Gravley
1a00fc3790
adding fixes (#1516) 
* adding fixes

* happy

* happy

* fix local files

* fix spacing

* i hate space

* spacing pt3 the space wars

* further down the bunny trail
 2021-05-04 11:33:21 -05:00
dependabot[bot]
63caefd599
Bump alpine/terragrunt from 0.14.5 to 0.14.7 (#1230) 
* Bump alpine/terragrunt from 0.14.5 to 0.14.7

Bumps alpine/terragrunt from 0.14.5 to 0.14.7.

Signed-off-by: dependabot[bot] <support@github.com>

* set log level to error

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
Co-authored-by: Marco Ferrari <ferrari.marco@gmail.com>
 2021-04-30 14:56:47 -05:00
Lukas Gravley
5f5904883d
remove tap and tests (#1496) 
* remove tap and tests

* fix proto

* remove dumb test
 2021-04-30 12:46:24 -05:00
Marco Ferrari
0c8db849aa
Implement a test suite with InSpec (#1466) 
* Implement a test suite with InSpec

* make ruby happy

* adding file

* Fix inspec and add make target

* Run inspec

* adding binaries

* make ruby happy

* fix linter order

* cleanup

* adding version check

* adding notes

* cleanup

* cleanup

* fixed r test

* fixed copy paste

* dynamic tests

* fix hash

* fix notation

* docker ps

* Fix makefile

* Fix makefile

Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
 2021-04-30 11:29:15 -05:00
Lukas Gravley
e0e4a67f3a
Certs (#1470) 
* adding cert

* update readme

* typo

* make exec

* spaces

* adding better way

* adding example

* make shell happy

* fix space

* adding notes

* bad var

* duh
 2021-04-26 09:00:42 -05:00
Erik Godding Boye
a908937c78
Add new ENV VAR to set ansible-lint config file (#1424) 2021-04-11 20:24:43 -07:00
Lukas Gravley
08a586cf3b
adding Python MyPy (#1401) 
* adding fun

* fix whitespace

* adding tests

* adding the array

* bug in file name

* fix tap

* makes no sense

* adding the hammer

* adding some extra protbuf
 2021-03-24 14:00:23 -05:00
Andreas Fritzler
1367534603
Allow to override github api url (#1395) 2021-03-23 13:26:14 -05:00
Lukas Gravley
3d39df7f0e
adding it (#1396) 
* adding it

* i kant read

* make go go away
 2021-03-23 12:02:16 -05:00
Andreas Fritzler
130b6ac1a5
Added support for custom github domain for status target url (#1367) 2021-03-15 15:19:54 -05:00
Tom Pansino
7b8e3189d8
Support custom markdownlint rules (#1306) 
* Support custom rules with markdownlint

* Add MARKDOWN_CUSTOM_RULE_GLOBS to README.md

* Fix shellcheck issues and use bash array for globs

* Fix shfmt issues

Co-authored-by: Gabriel Diaz <gabo.fdc@gmail.com>
 2021-03-10 09:06:06 -06:00
Antonio Yang
60e2561b15
Add clippy for rust (#1277) 
* Add clippy for Rust

* Update ARM test cases

- fix arm good test case
- update tap report

* Lint github workflows release config
 2021-03-08 14:13:04 -06:00
Gabriel Diaz
11720172cb
Fix get file diff on pr event (#1305) 
* Fix pr event sha

* Improve cmd

* Fix space
 2021-03-04 13:51:44 -06:00
Gabriel Diaz
46df94844c
Add debug info for multi status api calls (#1287) 
* Add debug info for multi status api calls

* Add test for clean action

* Add more verbose

* Test in action context

* Test use local build as action

* Improve debug for raw file array

* Fix shallow fetch

* Fix error messages on diff cmd

* Changed repeated code to function

* Fix quotes
 2021-03-02 08:29:12 -06:00
Antonio Yang
f47b363f71
Add rustfmt for Rust (#1250) 
* Add linter for Rust

- add 2015 edition
- add 2018 edition

* Add tap reports

- add tap reports
- fix good test case

* 1 command=lesslayers

Co-authored-by: Lukas Gravley <admiralawkbar@github.com>
 2021-02-26 08:47:21 -06:00
Marco Ferrari
b6bbc88e8e
Ignore files that are ignored by Git (#1185) 
* Ignore files that are ignored by Git

* Add missing continue statement

* Fix linting errors

* Fix linting errors

* like it

* like it

* Add the IGNORE_GITIGNORED_FILES variable

* Fix setting the Ansible directory when running tests

* Fix var export

* Update linter.sh

Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
 2021-02-18 12:15:50 -06:00
Marco Ferrari
ab8780a58f
Install, configure, and run jscpd. Add missing tests (#1032) 
Co-authored-by: Gabo <gabo.fdc@gmail.com>
Co-authored-by: Matt Desmond <beardofedu@github.com>
Co-authored-by: Lukas Gravley <admiralawkbar@github.com>
 2021-01-27 20:47:34 +01:00
Lukas Gravley
e11786a54c
Adding Flag for Possum (#1149) 
* adding a bad feature

* fix hadolint
 2021-01-19 11:03:14 -06:00
Lukas Gravley
193de39afd
Adding support for Prettier (#1118) 
* adding it

* fix spaces

* vars were backwards

* remove prettier from function test
 2021-01-04 11:07:57 -06:00
Marco Ferrari
156024e231
Simplify linter and worker by generalizing ansible-lint (#1035) 
Co-authored-by: Lukas Gravley <admiralawkbar@github.com>
 2020-12-04 16:04:09 -06:00
Cesar Rodriguez
0f9370c453
Fixes Terrascan to perform checks for all supported Terraform cloud providers (#1015) 
* updates to Terrascan v1.2.0

* updates command to explicitly scan terraform for all supported providers

* add no cache

* specify Pipfile

* verbose

* remove system

* remove cache

* put it back

* put it back

* clear

* adding cython

* more libs

* add system

Co-authored-by: Lukas Gravley <admiralawkbar@github.com>
Co-authored-by: SVN Migrator <someone@somewhere.com>
 2020-11-20 11:44:57 -06:00
Marco Ferrari
241f9f2cad
Harden testing (#982) 2020-11-20 09:12:31 -06:00
Lukas Gravley
cf19607c3c
Gherkin (#1011) 
* adding gherkin

* adding to array

* fix space

* Update Dockerfile

* adding rules

* adding rules

Co-authored-by: SVN Migrator <someone@somewhere.com>
 2020-11-19 09:54:20 -06:00
Lukas Gravley
fd154e1d13
give more memory (#992) 2020-11-12 11:45:04 -06:00
Lukas Gravley
7943ce1f54
break out: (#990) 
* break out:

* fix it

* fix source

* add them exports

* more path

* more path
 2020-11-12 11:27:34 -06:00
Marco Ferrari
b7e5dfce01 Fix shfmt errors 2020-11-06 23:10:09 +01:00
Marco Ferrari
c0441b2844 Use the already-defined linter names array to print linter versions 2020-11-04 10:26:05 +01:00
Lucas Gravley
2c9f8b1aa2 fixing logic 2020-11-03 10:06:33 -06:00
Marco Ferrari
3911130038 Fail on errors while getting linter versions 2020-11-02 21:54:26 +01:00
Lukas Gravley
5a04bd9875
Merge pull request #927 from github/fix-secondary-rules-file 
Don't override the secondary rules file path if available, don't reuse dirty values from previous iterations when loading rules files
 2020-11-02 08:58:06 -06:00
Gabo
e4b007cd40 Move validation to build time 2020-10-30 15:06:12 -05:00
Lukas Gravley
7f15e7a441
Merge branch 'master' into fix-secondary-rules-file 2020-10-30 10:25:58 -05:00
Marco Ferrari
e2f45db57d Initialize the LANGUAGE_LINTER_RULES value to avoid using leftovers from the previous iteration 2020-10-30 12:47:09 +01:00
Marco Ferrari
888bc7524e Don't override the secondary rules file path, if available 2020-10-30 12:15:16 +01:00
Gabo
997cfdcb02 Add notice warn and error log levels 2020-10-28 19:08:01 -05:00
Lucas Gravley
dbffb46526 adding tests 2020-10-28 10:22:55 -05:00
Ahmad Nassri
0396b9189b
fix: correct env variable name for JSX command (#890) 
fixes #889
 2020-10-23 09:17:25 +02:00
Callum
abb0901e2e
Fixed typo in missing linter rules. 2020-10-19 21:16:33 +02:00
Marco Ferrari
fcce194d34 Merge TestCodebase and LintCodebase 
Change-Id: I9a044fefe96e400b8e3320842b53fe97af2a7b40
 2020-10-17 16:12:55 +02:00
Marco Ferrari
5e25d5dcae Print linter commands 2020-10-15 16:45:18 +02:00
Marco Ferrari
2a4c89e92f Export LANGUAGE_LINTER_RULES 2020-10-15 16:45:18 +02:00
Marco Ferrari
fdb14fc19c Print environment variables before running linters 2020-10-15 16:45:18 +02:00
Marco Ferrari
df79a85546 Print environment variables before running linters 2020-10-15 16:45:18 +02:00
Marco Ferrari
4507a8e056 Add a debug instructions to check LANGUAGE_LINTER_RULES 2020-10-15 16:45:18 +02:00
Marco Ferrari
dfaeaf317d Simplify rules files loading, plus fixes 2020-10-15 16:45:18 +02:00
Lucas Gravley
7a775854e7 cleaner 2020-10-13 13:46:46 -05:00
Lucas Gravley
c3a1403fa0 fix tekton to not trigger kuber 2020-10-13 12:54:14 -05:00
Lucas Gravley
d8b13b0fd8 now with files 2020-10-13 10:21:23 -05:00
Marco Ferrari
c201c0f6d1 Dynamically invoke linters 2020-10-13 09:08:03 +02:00
Lukas Gravley
e8091a4ee9
Merge pull request #827 from PascalBourdier/ignore-kustomize-file 
ignore kustomize file with kubeval
 2020-10-12 10:36:45 -05:00
Lukas Gravley
6bde44e755
Merge pull request #824 from mshimokura/ecrc_file 
editorconfig-checker - Use .ecrc Files
 2020-10-12 10:24:00 -05:00
Michael Shimokura
a5cada70f8 Revert "rename the variable to EDITORCONFIG_CHECKER_FILE_NAME for clarity" 
This reverts commit 23a463867d.
 2020-10-09 09:13:37 -04:00
Michael Shimokura
23a463867d rename the variable to EDITORCONFIG_CHECKER_FILE_NAME for clarity 2020-10-09 09:02:12 -04:00
Pascal Bourdier
32a5945dd8 embedding the negation in the existing if 2020-10-09 11:53:34 +02:00
Pascal Bourdier
d975791bb9 ignore kustomize file with kubeval 
currently, kubeval doesn't support kustomize file

so kubeval returns a false-positive about a missing `metadata` key:
```
2020-10-09 06:19:19 [ERROR ]   Found errors in [kubeval] linter!
2020-10-09 06:19:19 [ERROR ]   [ERR  - .../kustomization.yml: Missing 'metadata' key]
2020-10-09 06:19:19 [ERROR ]   Linter CMD:[kubeval --strict .../kustomization.yml]
```
 2020-10-09 09:02:09 +02:00
Michael Shimokura
cd4798ea04 only assign EDITORCONFIG_FILE_NAME if not already assigned 2020-10-08 16:17:29 -04:00
Michael Shimokura
1312a3a3e4 use the .ecrc file 2020-10-08 15:27:47 -04:00
Tim Jones
a8746a7159 Add support for Terragrunt files 2020-10-08 18:18:22 +02:00
Marco Ferrari
a2b3938ea2 Dynamically load linter rules 2020-10-07 19:02:36 +02:00
Marco Ferrari
68e15659b8 Centralize file list building logic in buildFileList.sh 2020-10-07 16:36:49 +02:00
Marco Ferrari
d210896355 Set FILE_ARRAY_EDITORCONFIG 2020-10-03 00:33:01 +02:00
Marco Ferrari
e1b1c7d223 Dynamically initialize FILE_ARRAY variables 2020-10-02 23:02:47 +02:00
Marco Ferrari
973bfdea8e Initialize all log-related ASAP 2020-09-29 22:46:24 +02:00
Marco Ferrari
9371fab670 Remove unneeded variables and eval the rest 2020-09-29 22:33:11 +02:00
Lukas Gravley
18c32b7dca
Merge pull request #766 from mshimokura/editorconfig_lintall 
Lint all changed files with editorconfig-checker
 2020-09-28 08:38:51 -05:00
Lukas Gravley
167af0854e
Merge pull request #767 from kpj/master 
Fix various Snakemake related issues
 2020-09-28 08:36:48 -05:00
Marco Ferrari
31fd755fd7 Remove unneeded READ_ONLY_CHANGE_FLAG 2020-09-25 23:41:47 +02:00
kpj
9e7c84fbbb Fix various Snakemake related variable names 2020-09-24 16:06:12 +02:00
kpj
40f995365b Fix Snakefile regex 2020-09-24 15:55:47 +02:00
kpj
71ede6ccca Add missing 'GetLinterRules' calls 2020-09-24 15:54:24 +02:00
Michael Shimokura
12543b369b Lint all files with editorconfig-checker 
Since .editorconfig configuration files _could_ apply to any file, we
should pass in the RAW_FILE_ARRAY to it. This ensures that files of all
types are linted by editorconfig-checker.
 2020-09-24 09:02:24 -04:00
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
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
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