diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml
index a512fd2fab..e4eee511f2 100644
--- a/.github/workflows/build_and_test.yml
+++ b/.github/workflows/build_and_test.yml
@@ -47,6 +47,7 @@ jobs:
         os: [ ubuntu-latest, windows-latest, macos-latest ]
 
     steps:
+      - uses: actions/checkout@v2
       - name: Setup environment variables
         run: |
           cat pom.xml | grep "<version>.*</version>" | head -1 | awk -F'[><]' '{ printf "DIKTAT_VERSION=%s\n",$3 }' >> $GITHUB_ENV
@@ -67,7 +68,7 @@ jobs:
         continue-on-error: true
         if: ${{ runner.os == 'Linux' || runner.os == 'macOS' }}
         run: |
-          ./ktlint -R diktat-${{ env.DIKTAT_VERSION }}.jar --disabled_rules=standard "examples/maven/src/main/kotlin/Test.kt" &> out
+          ./ktlint -R diktat-${{ env.DIKTAT_VERSION }}.jar --disabled_rules=standard "examples/maven/src/main/kotlin/Test.kt" &> out.txt
         shell: bash
 
       - name: Run diKTat from cli on windows
@@ -80,9 +81,30 @@ jobs:
       - name: Check output
         id: cli-check
         run: |
-          if [ -f out.txt ]; then mv out.txt out; fi
-          cat out
-          grep -E "\[VARIABLE_NAME_INCORRECT_FORMAT\]" out
+          cat out.txt
+          grep -E "\[VARIABLE_NAME_INCORRECT_FORMAT\]" out.txt
+          rm out.txt
+        shell: bash
+
+      - name: Run diKTat from cli (absolute paths)
+        continue-on-error: true
+        if: ${{ runner.os == 'Linux' || runner.os == 'macOS' }}
+        run: |
+          ./ktlint -R diktat-${{ env.DIKTAT_VERSION }}.jar --disabled_rules=standard "$PWD/examples/maven/src/main/kotlin/Test.kt" &> out.txt
+        shell: bash
+
+      - name: Run diKTat from cli on windows (absolute paths)
+        continue-on-error: true
+        if: runner.os == 'Windows'
+        run: |
+          java.exe -jar ktlint -R diktat-${{ env.DIKTAT_VERSION }}.jar --disabled_rules=standard "%cd%/examples/maven/src/main/kotlin/Test.kt" > out.txt 2>&1
+        shell: cmd
+
+      - name: Check output (absolute paths)
+        id: cli-check
+        run: |
+          cat out.txt
+          grep -E "\[VARIABLE_NAME_INCORRECT_FORMAT\]" out.txt
         shell: bash
 
   build_and_test:
diff --git a/diktat-gradle-plugin/src/functionalTest/kotlin/org/cqfn/diktat/plugin/gradle/DiktatGradlePluginFunctionalTest.kt b/diktat-gradle-plugin/src/functionalTest/kotlin/org/cqfn/diktat/plugin/gradle/DiktatGradlePluginFunctionalTest.kt
index e130a1ec8d..245bafec59 100644
--- a/diktat-gradle-plugin/src/functionalTest/kotlin/org/cqfn/diktat/plugin/gradle/DiktatGradlePluginFunctionalTest.kt
+++ b/diktat-gradle-plugin/src/functionalTest/kotlin/org/cqfn/diktat/plugin/gradle/DiktatGradlePluginFunctionalTest.kt
@@ -159,6 +159,7 @@ class DiktatGradlePluginFunctionalTest {
     }
 
     @Test
+    @DisabledOnOs(OS.WINDOWS, disabledReason = "Because of short directory notation")
     fun `should execute diktatCheck with absolute paths`() {
         val path = testProjectDir.root
             .resolve("src/**/*.kt")