From 53f551c8b0240861ff337007095bf98bf4933e44 Mon Sep 17 00:00:00 2001
From: kpj <kpjkpjkpjkpjkpjkpj@gmail.com>
Date: Mon, 7 Sep 2020 17:26:58 +0200
Subject: [PATCH] [Snakemake] Add '--config' parameter to 'snakefmt' calls

---
 lib/linter.sh | 7 ++++---
 lib/worker.sh | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/lib/linter.sh b/lib/linter.sh
index 11bc1f43..0d098509 100755
--- a/lib/linter.sh
+++ b/lib/linter.sh
@@ -118,6 +118,9 @@ R_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${R_FILE_NAME}"
 # Ruby Vars
 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}"
+SNAKEMAKE_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SNAKEMAKE_FILE_NAME}"
 # 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
@@ -1855,9 +1858,7 @@ 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>
+  LintCodebase "SNAKEMAKE" "snakefmt" "snakefmt --config ${SNAKEMAKE_LINTER_RULES} --diff" ".*\.\(smk\)\$" "${FILE_ARRAY_SNAKEMAKE[@]}"
 fi
 
 ######################
diff --git a/lib/worker.sh b/lib/worker.sh
index 5437f479..fcaf6acd 100755
--- a/lib/worker.sh
+++ b/lib/worker.sh
@@ -702,7 +702,7 @@ function RunTestCases() {
   TestCodebase "RAKU" "raku" "raku -c" ".*\.\(raku\|rakumod\|rakutest\|pm6\|pl6\|p6\)\$" "raku"
   TestCodebase "RUBY" "rubocop" "rubocop -c ${RUBY_LINTER_RULES}" ".*\.\(rb\)\$" "ruby"
   TestCodebase "SHELL_SHFMT" "shfmt" "shfmt -d" ".*\.\(sh\|bash\|dash\|ksh\)\$" "shell_shfmt"
-  TestCodebase "SNAKEMAKE" "snakefmt" "snakefmt --diff" ".*\.\(smk\)\$" "snakemake"
+  TestCodebase "SNAKEMAKE" "snakefmt" "snakefmt --config ${SNAKEMAKE_LINTER_RULES} --diff" ".*\.\(smk\)\$" "snakemake"
   TestCodebase "STATES" "asl-validator" "asl-validator --json-path" ".*\.\(json\)\$" "states"
   TestCodebase "SQL" "sql-lint" "sql-lint --config ${SQL_LINTER_RULES}" ".*\.\(sql\)\$" "sql"
   TestCodebase "TERRAFORM" "tflint" "tflint -c ${TERRAFORM_LINTER_RULES}" ".*\.\(tf\)\$" "terraform"