mega-linter-runner -e ENABLE_LINTERS=YAML_PRETTIER,YAML_YAMLLINT only runs first linter, other linters are silently ignored

[vroad]

Describe the bug
mega-linter-runner (@9.4.0) runs only uses first linters, other linters are silently ignored.

npx mega-linter-runner -e ENABLE_LINTERS=YAML_PRETTIER,YAML_YAMLLINT gets translated to docker run command like this. (YAML_YAMLLINT passed as separate env var without value??)

Command: docker run --platform linux/amd64 --rm -v /var/run/docker.sock:/var/run/docker.sock:rw -v /home/nixos/Git/nixos-configuration-velox-wsl:/tmp/lint:rw -v /tmp/megalinter-1qbmLK/empty.env:/tmp/lint/.env:ro -e ENABLE_LINTERS=YAML_PRETTIER -e YAML_YAMLLINT ghcr.io/oxsecurity/megalinter:v9

On the other hand, mega-linter-runner works as expected if I set linters via .env instead.
example .env:

ENABLE_LINTERS=YAML_V8R,YAML_PRETTIER

npx mega-linter-ruuner translates this to a docker run command like this (which looks correct):

Command: docker run --platform linux/amd64 --rm -v /var/run/docker.sock:/var/run/docker.sock:rw -v /home/nixos/Git/nixos-configuration-velox-wsl:/tmp/lint:rw -v /tmp/megalinter-5mkuAV/empty.env:/tmp/lint/.env:ro -e ENABLE_LINTERS=YAML_V8R,YAML_PRETTIER -e ENABLE_LINTERS=YAML_PRETTIER -e ENABLE_LINTERS=YAML_YAMLLINT ghcr.io/oxsecurity/megalinter:v9

To Reproduce
Steps to reproduce the behavior:

1. npx mega-linter-runner -e ENABLE_LINTERS=YAML_PRETTIER,YAML_YAMLLINT

Expected behavior
Runs all linters specified with -e ENABLE_LINTERS option

Additional context

Logs when linters specified via -e ENABLE_LINTERS command line option

❯ npx mega-linter-runner -e ENABLE_LINTERS=YAML_PRETTIER,YAML_YAMLLINT
Pulling docker image ghcr.io/oxsecurity/megalinter:v9 ... 
INFO: this operation can be long during the first use of mega-linter-runner
The next runs, it will be immediate (thanks to docker cache !)
v9: Pulling from oxsecurity/megalinter
Digest: sha256:ed944524cb36342a3693f5297ab92aef7188beff0a20a396fe9e90b4dcbbacfb
Status: Image is up to date for ghcr.io/oxsecurity/megalinter:v9
ghcr.io/oxsecurity/megalinter:v9
Command: docker run --platform linux/amd64 --rm -v /var/run/docker.sock:/var/run/docker.sock:rw -v /home/nixos/Git/nixos-configuration-velox-wsl:/tmp/lint:rw -v /tmp/megalinter-1qbmLK/empty.env:/tmp/lint/.env:ro -e ENABLE_LINTERS=YAML_PRETTIER -e YAML_YAMLLINT ghcr.io/oxsecurity/megalinter:v9
Skipped setting git safe.directory DEFAULT_WORKSPACE:  ...
Setting git safe.directory default: /github/workspace ...
Setting git safe.directory to /tmp/lint ...
[MegaLinter init] ONE-SHOT RUN
[config] /tmp/lint/.mega-linter.yml + Environment variables

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==========================================================
=============   MegaLinter, by OX.security   =============
=========  https://ox.security?ref=megalinter  ===========
==========================================================

----------------------------------------------------------------------------------------------------
------------------------------------ MegaLinter, by OX Security ------------------------------------
----------------------------------------------------------------------------------------------------
 - Image Creation Date: 2026-02-28T10:08:53Z
 - Image Revision: 8fbdead70d1409964ab3d5afa885e18ee85388bb
 - Image Version: v9.4.0
----------------------------------------------------------------------------------------------------
The MegaLinter documentation can be found at:
 - https://megalinter.io/9.4.0
----------------------------------------------------------------------------------------------------
MegaLinter initialization
MegaLinter will analyze workspace [/tmp/lint]

JSON_ESLINT_PLUGIN_JSONC has been disabled in MegaLinter for the following reason: Bug in eslint-plugin-jsonc: <https://github.com/ota-meshi/eslint-plugin-jsonc/issues/328>
LUA_SELENE has been disabled in MegaLinter for the following reason: https://github.com/Kampfkarren/selene/issues/662
MAKEFILE_CHECKMAKE has been disabled in MegaLinter for the following reason: Security issues: <https://github.com/checkmake/checkmake/issues/99>
MARKDOWN_REMARK_LINT has been disabled in MegaLinter for the following reason: Bug in remark-lint: <https://github.com/remarkjs/remark-lint/issues/322>
PUPPET_PUPPET_LINT has been disabled in MegaLinter for the following reason: <https://github.com/puppetlabs/puppet-lint/issues/251>
SALESFORCE_LIGHTNING_FLOW_SCANNER has been disabled in MegaLinter for the following reason: Repo archived -> <https://github.com/Lightning-Flow-Scanner>
Skipped linters: ACTION_ACTIONLINT, ANSIBLE_ANSIBLE_LINT, API_SPECTRAL, ARM_ARM_TTK, BASH_EXEC, BASH_SHELLCHECK, BASH_SHFMT, BICEP_BICEP_LINTER, CLOJURE_CLJSTYLE, CLOJURE_CLJ_KONDO, CLOUDFORMATION_CFN_LINT, COFFEE_COFFEELINT, COPYPASTE_JSCPD, CPP_CLANG_FORMAT, CPP_CPPCHECK, CPP_CPPLINT, CSHARP_CSHARPIER, CSHARP_DOTNET_FORMAT, CSHARP_ROSLYNATOR, CSS_STYLELINT, C_CLANG_FORMAT, C_CPPCHECK, C_CPPLINT, DART_DARTANALYZER, DOCKERFILE_HADOLINT, EDITORCONFIG_EDITORCONFIG_CHECKER, ENV_DOTENV_LINTER, GHERKIN_GHERKIN_LINT, GO_GOLANGCI_LINT, GO_REVIVE, GRAPHQL_GRAPHQL_SCHEMA_LINTER, GROOVY_NPM_GROOVY_LINT, HTML_DJLINT, HTML_HTMLHINT, JAVASCRIPT_ES, JAVASCRIPT_PRETTIER, JAVASCRIPT_STANDARD, JAVA_CHECKSTYLE, JAVA_PMD, JSON_ESLINT_PLUGIN_JSONC, JSON_JSONLINT, JSON_NPM_PACKAGE_JSON_LINT, JSON_PRETTIER, JSON_V8R, JSX_ESLINT, KOTLIN_DETEKT, KOTLIN_KTLINT, KUBERNETES_HELM, KUBERNETES_KUBECONFORM, KUBERNETES_KUBESCAPE, LATEX_CHKTEX, LUA_LUACHECK, LUA_SELENE, LUA_STYLUA, MAKEFILE_CHECKMAKE, MARKDOWN_MARKDOWNLINT, MARKDOWN_MARKDOWN_TABLE_FORMATTER, MARKDOWN_REMARK_LINT, MARKDOWN_RUMDL, PERL_PERLCRITIC, PHP_PHPCS, PHP_PHPCSFIXER, PHP_PHPLINT, PHP_PHPSTAN, PHP_PSALM, POWERSHELL_POWERSHELL, POWERSHELL_POWERSHELL_FORMATTER, PROTOBUF_PROTOLINT, PUPPET_PUPPET_LINT, PYTHON_BANDIT, PYTHON_BLACK, PYTHON_FLAKE8, PYTHON_ISORT, PYTHON_MYPY, PYTHON_NBQA_MYPY, PYTHON_PYLINT, PYTHON_PYRIGHT, PYTHON_RUFF, PYTHON_RUFF_FORMAT, RAKU_RAKU, REPOSITORY_CHECKOV, REPOSITORY_DEVSKIM, REPOSITORY_DUSTILOCK, REPOSITORY_GITLEAKS, REPOSITORY_GIT_DIFF, REPOSITORY_GRYPE, REPOSITORY_KICS, REPOSITORY_KINGFISHER, REPOSITORY_LS_LINT, REPOSITORY_SECRETLINT, REPOSITORY_SEMGREP, REPOSITORY_SYFT, REPOSITORY_TRIVY, REPOSITORY_TRIVY_SBOM, REPOSITORY_TRUFFLEHOG, ROBOTFRAMEWORK_ROBOCOP, RST_RSTCHECK, RST_RSTFMT, RST_RST_LINT, RUBY_RUBOCOP, RUST_CLIPPY, R_LINTR, SALESFORCE_CODE_ANALYZER_APEX, SALESFORCE_CODE_ANALYZER_AURA, SALESFORCE_CODE_ANALYZER_LWC, SALESFORCE_LIGHTNING_FLOW_SCANNER, SALESFORCE_SFDX_SCANNER_APEX, SALESFORCE_SFDX_SCANNER_AURA, SALESFORCE_SFDX_SCANNER_LWC, SCALA_SCALAFIX, SNAKEMAKE_LINT, SNAKEMAKE_SNAKEFMT, SPELL_CODESPELL, SPELL_CSPELL, SPELL_LYCHEE, SPELL_PROSELINT, SPELL_VALE, SQL_SQLFLUFF, SQL_TSQLLINT, SWIFT_SWIFTLINT, TEKTON_TEKTON_LINT, TERRAFORM_TERRAFORM_FMT, TERRAFORM_TERRAGRUNT, TERRAFORM_TERRASCAN, TERRAFORM_TFLINT, TSX_ESLINT, TYPESCRIPT_ES, TYPESCRIPT_PRETTIER, TYPESCRIPT_STANDARD, VBDOTNET_DOTNET_FORMAT, XML_XMLLINT, YAML_V8R, YAML_YAMLLINT
To receive reports as email, please set variable EMAIL_REPORTER_EMAIL
[ApiReporter] Not enabled as API_REPORTER is not defined to true

MegaLinter now collects the files to analyse
Listing all files in directory [/tmp/lint], then filter with:
- File extensions: .yaml, .yml
- Excluding .gitignored files [2]: .env, result
Kept [4] files on [16] found files

+----MATCHING LINTERS---+------------+----------------+------------+
| Descriptor | Linter   | Criteria   | Matching files | Format/Fix |
+------------+----------+------------+----------------+------------+
| YAML       | prettier | .yml|.yaml | 4              | yes        |
+------------+----------+------------+----------------+------------+

✅ Linted [YAML] files with [prettier] successfully - (0.32s)
- Using [prettier v3.8.1] https://megalinter.io/9.4.0/descriptors/yaml_prettier
- MegaLinter key: [YAML_PRETTIER]
- Rules config: identified by [prettier]
- Number of files analyzed: [4]
- CWD: [/tmp/lint]
- Command: [prettier --write .github/workflows/claude.yml .github/workflows/mega-linter.yml .mega-linter.yml .pre-commit-config.yaml]

[Updated Sources Reporter] No source file has been formatted or fixed

+----SUMMARY-+----------+---------------+-------+-------+--------+----------+--------------+
| Descriptor | Linter   | Mode          | Files | Fixed | Errors | Warnings | Elapsed time |
+------------+----------+---------------+-------+-------+--------+----------+--------------+
| ✅ YAML    | prettier | list_of_files |     4 |     0 |      0 |        0 | 0.32s        |
+------------+----------+---------------+-------+-------+--------+----------+--------------+

You could have same capabilities but better runtime performances if you use a MegaLinter flavor:
- [formatters] oxsecurity/megalinter/flavors/formatters@v9 (19 linters) https://megalinter.io/9.4.0/flavors/formatters/
- [ci_light] oxsecurity/megalinter/flavors/ci_light@v9 (22 linters) https://megalinter.io/9.4.0/flavors/ci_light/
- [documentation] oxsecurity/megalinter/flavors/documentation@v9 (51 linters) https://megalinter.io/9.4.0/flavors/documentation/
Your project could benefit from a custom flavor, which would allow you to run only the linters you need, and thus improve runtime performances. (Skip this info by defining `FLAVOR_SUGGESTIONS: false`)
- Documentation: https://megalinter.io/9.4.0/custom-flavors/
- Command: `npx mega-linter-runner@9.4.0 --custom-flavor-setup --custom-flavor-linters YAML_PRETTIER`

✅ Successfully linted all files without errors