From 1e453be7fa22a2df9c4858b0dc5e22ef544b422f Mon Sep 17 00:00:00 2001
From: kpj <kpjkpjkpjkpjkpjkpj@gmail.com>
Date: Mon, 7 Sep 2020 16:49:07 +0200
Subject: [PATCH] [Snakemake] Update codebase

---
 .github/linters/.snakefmt.toml |  0
 Dockerfile                     |  1 +
 TEMPLATES/.snakefmt.toml       |  0
 lib/buildFileList.sh           | 13 +++++++++++++
 lib/linter.sh                  | 14 ++++++++++++++
 5 files changed, 28 insertions(+)
 create mode 100644 .github/linters/.snakefmt.toml
 create mode 100644 TEMPLATES/.snakefmt.toml

diff --git a/.github/linters/.snakefmt.toml b/.github/linters/.snakefmt.toml
new file mode 100644
index 00000000..e69de29b
diff --git a/Dockerfile b/Dockerfile
index 7b737996..e0fcaafa 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -380,6 +380,7 @@ ENV ACTIONS_RUNNER_DEBUG=${ACTIONS_RUNNER_DEBUG} \
     VALIDATE_RAKU=${VALIDATE_RAKU} \
     VALIDATE_RUBY=${VALIDATE_RUBY} \
     VALIDATE_SHELL_SHFMT=${VALIDATE_SHELL_SHFMT} \
+    VALIDATE_SNAKEMAKE=${VALIDATE_SNAKEMAKE} \
     VALIDATE_STATES=${VALIDATE_STATES} \
     VALIDATE_SQL=${VALIDATE_SQL} \
     VALIDATE_TERRAFORM=${VALIDATE_TERRAFORM} \
diff --git a/TEMPLATES/.snakefmt.toml b/TEMPLATES/.snakefmt.toml
new file mode 100644
index 00000000..e69de29b
diff --git a/lib/buildFileList.sh b/lib/buildFileList.sh
index 13371ef6..a8452a2f 100755
--- a/lib/buildFileList.sh
+++ b/lib/buildFileList.sh
@@ -484,6 +484,19 @@ function BuildFileList() {
       ##########################################################
       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 #
     #####################
diff --git a/lib/linter.sh b/lib/linter.sh
index 78d2f5bf..11bc1f43 100755
--- a/lib/linter.sh
+++ b/lib/linter.sh
@@ -207,6 +207,7 @@ VALIDATE_RAKU="${VALIDATE_RAKU}"                                     # Boolean t
 VALIDATE_RUBY="${VALIDATE_RUBY}"                                     # 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_SNAKEMAKE="${VALIDATE_SNAKEMAKE}"                           # Boolean to check Snakefiles
 VALIDATE_SQL="${VALIDATE_SQL}"                                       # Boolean to validate language
 VALIDATE_TERRAFORM="${VALIDATE_TERRAFORM}"                           # Boolean to validate language
 VALIDATE_TERRAFORM_TERRASCAN="${VALIDATE_TERRAFORM_TERRASCAN}"       # Boolean to validate language
@@ -1846,6 +1847,19 @@ if [ "${VALIDATE_SHELL_SHFMT}" == "true" ]; then
   fi
 fi
 
+#####################
+# 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 #
 ######################