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Merge pull request #767 from kpj/master

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Fix various Snakemake related issues
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Lukas Gravley 2020-09-28 08:36:48 -05:00 committed by GitHub
commit 167af0854e
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3 changed files with 10 additions and 6 deletions
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2
Dockerfile
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@ -346,7 +346,7 @@ ENV ACTIONS_RUNNER_DEBUG=${ACTIONS_RUNNER_DEBUG} \
OUTPUT_FOLDER=${OUTPUT_FOLDER} \
OUTPUT_FORMAT=${OUTPUT_FORMAT} \
RUN_LOCAL=${RUN_LOCAL} \
SNAKEMAKE_CONFIG_FILE=${SNAKEMAKE_CONFIG_FILE} \
SNAKEMAKE_SNAKEFMT_CONFIG_FILE=${SNAKEMAKE_SNAKEFMT_CONFIG_FILE} \
TEST_CASE_RUN=${TEST_CASE_RUN} \
VALIDATE_ALL_CODEBASE=${VALIDATE_ALL_CODEBASE} \
VALIDATE_ANSIBLE=${VALIDATE_ANSIBLE} \

2
README.md
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@ -222,7 +222,7 @@ But if you wish to select or exclude specific linters, we give you full control
| **PYTHON_FLAKE8_CONFIG_FILE** | `.flake8` | Filename for [flake8 configuration](https://flake8.pycqa.org/en/latest/user/configuration.html) (ex: `.flake8`, `tox.ini`) |
| **PYTHON_BLACK_CONFIG_FILE** | `.python-black` | Filename for [black configuration](https://github.com/psf/black/blob/master/docs/compatible_configs.md) (ex: `.isort.cfg`, `pyproject.toml`) |
| **RUBY_CONFIG_FILE** | `.ruby-lint.yml` | Filename for [rubocop configuration](https://docs.rubocop.org/rubocop/configuration.html) (ex: `.ruby-lint.yml`, `.rubocop.yml`) |
| **SNAKEMAKE_CONFIG_FILE** | `.snakefmt.toml` | Filename for [Snakemake configuration](https://github.com/snakemake/snakefmt#configuration) (ex: `pyproject.toml`, `.snakefmt.toml`) |
| **SNAKEMAKE_SNAKEFMT_CONFIG_FILE**| `.snakefmt.toml` | Filename for [Snakemake configuration](https://github.com/snakemake/snakefmt#configuration) (ex: `pyproject.toml`, `.snakefmt.toml`) |
| **TYPESCRIPT_ES_CONFIG_FILE** | `.eslintrc.yml` | Filename for [eslint configuration](https://eslint.org/docs/user-guide/configuring#configuration-file-formats) (ex: `.eslintrc.yml`, `.eslintrc.json`) |
| **VALIDATE_ALL_CODEBASE** | `true` | Will parse the entire repository and find all files to validate across all types. **NOTE:** When set to `false`, only **new** or **edited** files will be parsed for validation. |
| **VALIDATE_ANSIBLE** | `true` | Flag to enable or disable the linting process of the Ansible language. |

12
lib/linter.sh
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@ -119,8 +119,8 @@ R_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${R_FILE_NAME}" # Path to the R lint r
RUBY_FILE_NAME="${RUBY_CONFIG_FILE:-.ruby-lint.yml}" # Name of the file
RUBY_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${RUBY_FILE_NAME}" # Path to the ruby lint rules
# Snakemake Vars
SNAKEMAKE_FILE_NAME="${SNAKEMAKE_CONFIG_FILE:-.snakefmt.toml}" # Name of the file
SNAKEMAKE_SNAKEFMT_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SNAKEMAKE_FILE_NAME}" # Path to the snakemake lint rules
SNAKEMAKE_SNAKEFMT_FILE_NAME="${SNAKEMAKE_SNAKEFMT_CONFIG_FILE:-.snakefmt.toml}" # Name of the file
SNAKEMAKE_SNAKEFMT_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SNAKEMAKE_SNAKEFMT_FILE_NAME}" # Path to the snakemake lint rules
# SQL Vars
SQL_FILE_NAME=".sql-config.json" # Name of the file
SQL_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SQL_FILE_NAME}" # Path to the SQL lint rules
@ -1310,6 +1310,10 @@ GetLinterRules "PYTHON_BLACK"
GetLinterRules "R"
# Get Ruby rules
GetLinterRules "RUBY"
# Get Snakemake lint rules
GetLinterRules "SNAKEMAKE_LINT"
# Get Snakemake snakefmt rules
GetLinterRules "SNAKEMAKE_SNAKEFMT"
# Get SQL rules
GetLinterRules "SQL"
# Get Terraform rules
@ -1932,7 +1936,7 @@ if [ "${VALIDATE_SNAKEMAKE_LINT}" == "true" ]; then
# Lint the files with snakefmt #
################################
# LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILTER_REGEX_INCLUDE" "FILTER_REGEX_EXCLUDE" "FILE_ARRAY"
LintCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" "\(Snakefile|.*\.smk\)\$" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}" "${FILE_ARRAY_SNAKEMAKE[@]}"
LintCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" ".*\(Snakefile\|\.smk\)\$" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}" "${FILE_ARRAY_SNAKEMAKE[@]}"
fi
@ -1944,7 +1948,7 @@ if [ "${VALIDATE_SNAKEMAKE_SNAKEFMT}" == "true" ]; then
# Lint the files with snakefmt #
################################
# LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILTER_REGEX_INCLUDE" "FILTER_REGEX_EXCLUDE" "FILE_ARRAY"
LintCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --check --compact-diff" "\(Snakefile|.*\.smk\)\$" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}" "${FILE_ARRAY_SNAKEMAKE[@]}"
LintCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --check --compact-diff" ".*\(Snakefile\|\.smk\)\$" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}" "${FILE_ARRAY_SNAKEMAKE[@]}"
fi
######################