fix syntax

nf-core · Jan 9, 2025 · bca2025 · bca2025
1 parent cc9819b
commit bca2025
Showing 1 changed file with 25 additions and 26 deletions.
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -101,32 +101,31 @@ jobs:
             --arg profile "${{ matrix.profile }}" \
             --argjson input_paths "$PATHS" \
             '
-              def get_skip_list: inputs | .[$profile] // [];
-              def log_debug($msg): $msg | "::debug::" + . ;
-
-              # Get skip list and filter
-              get_skip_list as $skip_patterns |
-
-              # Log skip patterns
-              ($skip_patterns | map("  - " + .) | join("\n") | log_debug("Skip patterns:\n" + .)) | debug |
-
-              # Do the filtering
-              $input_paths | map(
-                . as $path |
-                select($skip_patterns | all(. as $pattern | ($path | startswith($pattern)) | not))
-              ) as $result |
-
-              # Log skipped paths
-              (if ($input_paths - $result) | length > 0 then
-                ($input_paths - $result) | map("  - " + .) | join("\n") | log_debug("Skipped:\n" + .)
-              else
-                log_debug("No paths skipped")
-              end) | debug |
-
-              $result
-              ' .github/skip_nf_test.json)
-
-            echo "filtered_paths=${FILTERED}" >> $GITHUB_OUTPUT
+            def get_skip_list: inputs | .[$profile] // [];
+            def log_debug($msg): $msg | "::debug::" + . ;
+
+            # Get skip list and filter
+            get_skip_list as $skip_patterns |
+
+            # Log skip patterns
+            ($skip_patterns | map(" - " + .) | join("\n") | log_debug("Skip patterns:\n" + .)) | debug |
+
+            # Do the filtering
+            $input_paths | map(
+              . as $path |
+              select($skip_patterns | all(. as $pattern | ($path | startswith($pattern)) | not))
+            ) as $result |
+
+            # Log skipped paths
+            (if ($input_paths - $result) | length > 0 then
+              ($input_paths - $result) | map(" - " + .) | join("\n") | log_debug("Skipped:\n" + .)
+            else
+              log_debug("No paths skipped")
+            end) | debug |
+
+            $result
+            ' .github/skip_nf_test.json)
+          echo "filtered_paths=${FILTERED}" >> $GITHUB_OUTPUT
 
       - name: Run nf-test Action
         if: ${{steps.filter.outputs.filtered_paths != '[]'}}