fix: batch files in lint hook to avoid ARG_MAX on large repos

nextflow-lint-hook

@@ -35,11 +35,28 @@ if [[ ${#files[@]} -eq 0 ]]; then
     exit 0
 fi
 
-# Run nextflow lint with flags followed by files
-# Use ${args[@]+"${args[@]}"} for bash 3.x compatibility (empty array + set -u)
-if nextflow lint ${args[@]+"${args[@]}"} "${files[@]}"; then
-    echo "✅ Nextflow lint passed"
-else
+# Run nextflow lint in batches to avoid "Argument list too long" (E2BIG)
+# when pre-commit passes thousands of files on large repos.
+# Capture output so we can filter per-batch success noise while
+# always showing errors, warnings, and any other diagnostic output.
+batch_size=200
+lint_failed=false
+all_output=""
+
+for ((i=0; i<${#files[@]}; i+=batch_size)); do
+    batch=("${files[@]:i:batch_size}")
+    # Use ${args[@]+...} for bash 3.x compatibility (empty array + set -u)
+    batch_output=$(nextflow lint ${args[@]+"${args[@]}"} "${batch[@]}" 2>&1) || lint_failed=true
+    all_output+="$batch_output"$'\n'
+done
+
+# Always display output (errors are never hidden), but filter out
+# the per-batch success summaries to keep CI logs readable.
+printf '%s' "$all_output" | grep -vE 'Nextflow linting complete!|files had no errors' || true
+
+if $lint_failed; then
     echo "❌ Nextflow lint failed"
     exit 1
+else
+    echo "✅ Nextflow lint passed (${#files[@]} files)"
 fi