diff --git a/.github/workflows/tools.yaml b/.github/workflows/tools.yaml
index 32fd645..7a65209 100644
--- a/.github/workflows/tools.yaml
+++ b/.github/workflows/tools.yaml
@@ -182,6 +182,11 @@ jobs:
       continue-on-error: true
     - name: check if all test tools were linted
       run: |
+        set -x
+        # check if the ToolIDValid linter is called (no of tools - 1 ) times, i.e. is skipped once
+        if [ "$(grep -c ToolIDValid lint_report.txt)" != "2" ]; then
+          echo "expecting exactly 2 tests for ToolIDValid"; exit 1; 
+        fi
         grep tool1 lint_report.txt
         grep tool2 lint_report.txt
         grep "ERROR: Error 'HTTPConnectionPool" lint_report.txt
diff --git a/README.md b/README.md
index 97b4bfa..e3cdb37 100644
--- a/README.md
+++ b/README.md
@@ -42,6 +42,8 @@ Tools/workflows in a path that has a prefix in:
 
 Tools and workflows are discovered in all directories, except for `packages/` and `deprecated/`. These directories may be absent.
 
+A global `.lint_skip` file and per repo `.lint_skip` files can be used to list tool/workflow linters that should be skipped.
+
 Setup mode
 ----------
 
diff --git a/planemo_ci_actions.sh b/planemo_ci_actions.sh
index 437fdbd..8247442 100755
--- a/planemo_ci_actions.sh
+++ b/planemo_ci_actions.sh
@@ -110,10 +110,13 @@ fi
 # - check if each tool is in a repo (i.e. if `.shed.yml` is present)
 if [ "$MODE" == "lint" ]; then
   lint_fail=false
+  touch .lint_skip
   mapfile -t REPO_ARRAY < repository_list.txt
   for DIR in "${REPO_ARRAY[@]}"; do
     if [ "$WORKFLOWS" != "true" ]; then
-      (planemo shed_lint --tools --ensure_metadata --urls --report_level "$REPORT_LEVEL" --fail_level "$FAIL_LEVEL" --recursive "$DIR" "${ADDITIONAL_PLANEMO_OPTIONS[@]}" | tee -a lint_report.txt) || lint_fail=true
+      cat .lint_skip >> "$DIR"/.lint_skip
+      cat "$DIR"/.lint_skip
+      (planemo shed_lint --tools --ensure_metadata --urls --skip_file "$DIR"/.lint_skip --report_level "$REPORT_LEVEL" --fail_level "$FAIL_LEVEL" --recursive "$DIR" "${ADDITIONAL_PLANEMO_OPTIONS[@]}" | tee -a lint_report.txt) || lint_fail=true
     else
       (planemo workflow_lint --report_level "$REPORT_LEVEL" --fail_level "$FAIL_LEVEL" "$DIR" "${ADDITIONAL_PLANEMO_OPTIONS[@]}" | tee -a lint_report.txt) || lint_fail=true
     fi
diff --git a/test/tools/tool1/.lint_skip b/test/tools/tool1/.lint_skip
new file mode 100644
index 0000000..780125a
--- /dev/null
+++ b/test/tools/tool1/.lint_skip
@@ -0,0 +1 @@
+ToolIDValid
\ No newline at end of file