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[Snakemake] Update codebase

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kpj 2020-09-07 16:49:07 +02:00
parent 15eec55117
commit 1e453be7fa
5 changed files with 28 additions and 0 deletions
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0
.github/linters/.snakefmt.toml vendored Normal file
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1
Dockerfile
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@ -380,6 +380,7 @@ ENV ACTIONS_RUNNER_DEBUG=${ACTIONS_RUNNER_DEBUG} \
VALIDATE_RAKU=${VALIDATE_RAKU} \ VALIDATE_RAKU=${VALIDATE_RAKU} \
VALIDATE_RUBY=${VALIDATE_RUBY} \ VALIDATE_RUBY=${VALIDATE_RUBY} \
VALIDATE_SHELL_SHFMT=${VALIDATE_SHELL_SHFMT} \ VALIDATE_SHELL_SHFMT=${VALIDATE_SHELL_SHFMT} \
VALIDATE_SNAKEMAKE=${VALIDATE_SNAKEMAKE} \
VALIDATE_STATES=${VALIDATE_STATES} \ VALIDATE_STATES=${VALIDATE_STATES} \
VALIDATE_SQL=${VALIDATE_SQL} \ VALIDATE_SQL=${VALIDATE_SQL} \
VALIDATE_TERRAFORM=${VALIDATE_TERRAFORM} \ VALIDATE_TERRAFORM=${VALIDATE_TERRAFORM} \

0
TEMPLATES/.snakefmt.toml Normal file
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13
lib/buildFileList.sh
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@ -484,6 +484,19 @@ function BuildFileList() {
########################################################## ##########################################################
READ_ONLY_CHANGE_FLAG=1 READ_ONLY_CHANGE_FLAG=1
###########################
# Get the SNAKEMAKE files #
###########################
elif [ "${FILE_TYPE}" == "smk" ]; then
################################
# Append the file to the array #
################################
FILE_ARRAY_SNAKEMAKE+=("${FILE}")
##########################################################
# Set the READ_ONLY_CHANGE_FLAG since this could be exec #
##########################################################
READ_ONLY_CHANGE_FLAG=1
##################### #####################
# Get the SQL files # # Get the SQL files #
##################### #####################

14
lib/linter.sh
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@ -207,6 +207,7 @@ VALIDATE_RAKU="${VALIDATE_RAKU}" # Boolean t
VALIDATE_RUBY="${VALIDATE_RUBY}" # Boolean to validate language VALIDATE_RUBY="${VALIDATE_RUBY}" # Boolean to validate language
VALIDATE_STATES="${VALIDATE_STATES}" # Boolean to validate language VALIDATE_STATES="${VALIDATE_STATES}" # Boolean to validate language
VALIDATE_SHELL_SHFMT="${VALIDATE_SHELL_SHFMT}" # Boolean to check Shell files against editorconfig VALIDATE_SHELL_SHFMT="${VALIDATE_SHELL_SHFMT}" # Boolean to check Shell files against editorconfig
VALIDATE_SNAKEMAKE="${VALIDATE_SNAKEMAKE}" # Boolean to check Snakefiles
VALIDATE_SQL="${VALIDATE_SQL}" # Boolean to validate language VALIDATE_SQL="${VALIDATE_SQL}" # Boolean to validate language
VALIDATE_TERRAFORM="${VALIDATE_TERRAFORM}" # Boolean to validate language VALIDATE_TERRAFORM="${VALIDATE_TERRAFORM}" # Boolean to validate language
VALIDATE_TERRAFORM_TERRASCAN="${VALIDATE_TERRAFORM_TERRASCAN}" # Boolean to validate language VALIDATE_TERRAFORM_TERRASCAN="${VALIDATE_TERRAFORM_TERRASCAN}" # Boolean to validate language
@ -1846,6 +1847,19 @@ if [ "${VALIDATE_SHELL_SHFMT}" == "true" ]; then
fi fi
fi fi
#####################
# SNAKEMAKE LINTING #
#####################
if [ "${VALIDATE_SNAKEMAKE}" == "true" ]; then
################################
# Lint the files with snakefmt #
################################
# LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILE_ARRAY"
LintCodebase "SNAKEMAKE" "snakefmt" "snakefmt --diff" ".*\.\(smk\)\$" "${FILE_ARRAY_SNAKEMAKE[@]}"
# TODO: add --config <path>
fi
###################### ######################
# AWS STATES LINTING # # AWS STATES LINTING #
###################### ######################