From bfc196854d697379584a1ba06969d5411ec574c5 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Tue, 3 Mar 2026 15:06:27 +0100
Subject: [PATCH 1/9] Support Nextflow typed syntax for process inputs/outputs

Add parsing support for Nextflow's typed I/O declarations
(nextflow.preview.types = true) which use a different syntax than
traditional DSL2:

- Typed tuple inputs: (meta, bam): Tuple<Map, Path>
- Typed simple inputs: x: Integer, bam: Path
- Named assignment outputs: txt = tuple(meta, file("*.txt"))
- Topic sections: topic:/>> 'name' as section delimiters

Also adds comprehensive test suite for nf_parser module (53 tests)
covering both traditional and typed syntax patterns.

Fixes issue where pipelines using typed syntax would generate
documentation with no inputs or outputs listed.
---
 src/nf_docs/nf_parser.py | 135 ++++++++++-
 tests/test_nf_parser.py  | 473 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 604 insertions(+), 4 deletions(-)
 create mode 100644 tests/test_nf_parser.py

diff --git a/src/nf_docs/nf_parser.py b/src/nf_docs/nf_parser.py
index 1701879..1f03591 100644
--- a/src/nf_docs/nf_parser.py
+++ b/src/nf_docs/nf_parser.py
@@ -8,6 +8,10 @@
 import re
 from dataclasses import dataclass, field
 
+# Traditional Nextflow input qualifiers that should not be treated as typed variable names.
+# Used to prevent false matches like "each: sample" being parsed as typed input "each" of type "sample".
+_TRADITIONAL_QUALIFIERS = frozenset({"val", "path", "file", "env", "stdin", "tuple", "each"})
+
 
 @dataclass
 class ParsedInput:
@@ -84,13 +88,17 @@ def parse_process_hover(hover_text: str) -> ParsedProcess | None:
     process = ParsedProcess(name=name_match.group(1))
 
     # Extract input section
-    input_match = re.search(r"input:\s*(.*?)(?:output:|script:|shell:|exec:|\})", code, re.DOTALL)
+    input_match = re.search(
+        r"input:\s*(.*?)(?:output:|topic:|script:|shell:|exec:|\})", code, re.DOTALL
+    )
     if input_match:
         input_block = input_match.group(1)
         process.inputs = _parse_input_declarations(input_block)
 
     # Extract output section
-    output_match = re.search(r"output:\s*(.*?)(?:script:|shell:|exec:|when:|\})", code, re.DOTALL)
+    output_match = re.search(
+        r"output:\s*(.*?)(?:topic:|script:|shell:|exec:|when:|\})", code, re.DOTALL
+    )
     if output_match:
         output_block = output_match.group(1)
         process.outputs = _parse_output_declarations(output_block)
@@ -118,11 +126,49 @@ def _parse_input_declarations(block: str) -> list[ParsedInput]:
 
 
 def _parse_single_input(line: str) -> ParsedInput | None:
-    """Parse a single input declaration line."""
+    """Parse a single input declaration line.
+
+    Handles both traditional DSL2 syntax and typed syntax:
+      - Traditional: ``tuple val(meta), path(reads)``
+      - Typed tuple: ``(meta, bam): Tuple<Map, Path>``
+      - Typed simple: ``x: Integer``, ``bam: Path``
+    """
     line = line.strip()
     if not line:
         return None
 
+    # Handle typed destructured tuple: (meta, bam): Tuple<Map, Path>
+    typed_tuple_match = re.match(r"\(([^)]+)\)\s*:\s*Tuple\s*<([^>]+)>", line)
+    if typed_tuple_match:
+        names_str = typed_tuple_match.group(1)
+        types_str = typed_tuple_match.group(2)
+        names = [n.strip() for n in names_str.split(",")]
+        types = [t.strip() for t in types_str.split(",")]
+        # Build descriptive components pairing names with their types
+        parts = []
+        for i, name in enumerate(names):
+            if i < len(types):
+                type_name = types[i]
+                # Map Nextflow types to traditional qualifiers for display
+                qualifier = _typed_to_qualifier(type_name)
+                parts.append(f"{qualifier}({name})")
+            else:
+                parts.append(f"val({name})")
+        return ParsedInput(
+            name=", ".join(parts),
+            type="tuple",
+            qualifier=f"Tuple<{types_str}>",
+        )
+
+    # Handle typed simple input: x: Integer, bam: Path
+    # Exclude traditional Nextflow qualifiers that could false-match (e.g. "each: sample")
+    typed_simple_match = re.match(r"(\w+)\s*:\s*(\w+)$", line)
+    if typed_simple_match and typed_simple_match.group(1) not in _TRADITIONAL_QUALIFIERS:
+        name = typed_simple_match.group(1)
+        type_name = typed_simple_match.group(2)
+        qualifier = _typed_to_qualifier(type_name)
+        return ParsedInput(name=name, type=qualifier, qualifier=type_name)
+
     # Handle tuple inputs: tuple val(meta), path(reads)
     if line.startswith("tuple"):
         # Extract components
@@ -154,6 +200,22 @@ def _parse_single_input(line: str) -> ParsedInput | None:
     return None
 
 
+def _typed_to_qualifier(type_name: str) -> str:
+    """Map a Nextflow type annotation to a traditional qualifier name.
+
+    Args:
+        type_name: The type annotation (e.g. ``Path``, ``Map``, ``Integer``).
+
+    Returns:
+        The corresponding traditional qualifier (``val``, ``path``, etc.).
+    """
+    path_types = {"Path", "File"}
+    if type_name in path_types:
+        return "path"
+    # Everything else maps to val (Map, Integer, String, Boolean, etc.)
+    return "val"
+
+
 def _parse_output_declarations(block: str) -> list[ParsedOutput]:
     """Parse output declarations from an output block."""
     outputs = []
@@ -174,11 +236,30 @@ def _parse_output_declarations(block: str) -> list[ParsedOutput]:
 
 
 def _parse_single_output(line: str) -> ParsedOutput | None:
-    """Parse a single output declaration line."""
+    """Parse a single output declaration line.
+
+    Handles both traditional DSL2 syntax and typed/named assignment syntax:
+      - Traditional: ``tuple val(meta), path("*.html"), emit: html``
+      - Named assignment: ``txt = tuple(meta, file("*_svpileup.txt"))``
+      - Named simple: ``bam = file("*.bam")``
+      - Topic publish: ``>> 'topic_name'``
+    """
     line = line.strip()
     if not line:
         return None
 
+    # Skip topic publish lines: >> 'topic_name'
+    if line.startswith(">>"):
+        return None
+
+    # Handle named assignment outputs: name = tuple(meta, file("*_svpileup.txt"))
+    # or: name = file("*.bam"), name = val(something)
+    named_match = re.match(r"(\w+)\s*=\s*(.+)", line)
+    if named_match:
+        emit_name = named_match.group(1)
+        rhs = named_match.group(2).strip()
+        return _parse_named_output(emit_name, rhs)
+
     # Extract emit name if present
     emit_match = re.search(r"emit:\s*(\w+)", line)
     emit_name = emit_match.group(1) if emit_match else ""
@@ -208,6 +289,52 @@ def _parse_single_output(line: str) -> ParsedOutput | None:
     return None
 
 
+def _parse_named_output(emit_name: str, rhs: str) -> ParsedOutput:
+    """Parse the right-hand side of a named output assignment.
+
+    Handles patterns like:
+      - ``tuple(meta, file("*_svpileup.txt"))``
+      - ``file("*.bam")``
+      - ``val(something)``
+      - ``path("versions.yml")``
+
+    Args:
+        emit_name: The variable name (used as the emit name).
+        rhs: The right-hand side expression after ``=``.
+
+    Returns:
+        A ParsedOutput with the emit name and parsed type/components.
+    """
+    rhs = rhs.strip()
+
+    # Handle tuple(...): tuple(meta, file("*_svpileup.txt"))
+    tuple_match = re.match(r"tuple\s*\((.+)\)\s*$", rhs)
+    if tuple_match:
+        inner = tuple_match.group(1)
+        # Extract typed components: file("..."), val(...), path("...")
+        components = re.findall(r"(val|path|file|env)\s*\(([^)]+)\)", inner)
+        if components:
+            parts = []
+            for comp_type, comp_name in components:
+                parts.append(f"{comp_type}({comp_name})")
+            name = ", ".join(parts)
+        else:
+            # Plain names: tuple(meta, bam)
+            names = [n.strip() for n in inner.split(",")]
+            name = ", ".join(f"val({n})" for n in names)
+        return ParsedOutput(name=name, type="tuple", emit=emit_name)
+
+    # Handle simple: file("*.bam"), path("versions.yml"), val(x)
+    simple_match = re.match(r"(val|path|file|env|stdout)\s*\(([^)]*)\)", rhs)
+    if simple_match:
+        output_type = simple_match.group(1)
+        name = simple_match.group(2).strip().strip("'\"") if simple_match.group(2) else output_type
+        return ParsedOutput(name=name, type=output_type, emit=emit_name)
+
+    # Fallback: treat entire rhs as the name
+    return ParsedOutput(name=rhs, type="val", emit=emit_name)
+
+
 def parse_workflow_hover(hover_text: str) -> ParsedWorkflow | None:
     """
     Parse a workflow definition from LSP hover content.
diff --git a/tests/test_nf_parser.py b/tests/test_nf_parser.py
new file mode 100644
index 0000000..07af079
--- /dev/null
+++ b/tests/test_nf_parser.py
@@ -0,0 +1,473 @@
+"""Tests for the Nextflow code parser."""
+
+from nf_docs.nf_parser import (
+    ParsedInput,
+    _parse_named_output,
+    _parse_single_input,
+    _parse_single_output,
+    _typed_to_qualifier,
+    parse_process_hover,
+    parse_workflow_hover,
+)
+
+
+class TestParseSingleInput:
+    """Tests for _parse_single_input."""
+
+    def test_empty_line(self):
+        assert _parse_single_input("") is None
+        assert _parse_single_input("   ") is None
+
+    def test_simple_val(self):
+        result = _parse_single_input("val(x)")
+        assert result == ParsedInput(name="x", type="val")
+
+    def test_simple_path(self):
+        result = _parse_single_input("path(reads)")
+        assert result == ParsedInput(name="reads", type="path")
+
+    def test_simple_env(self):
+        result = _parse_single_input("env(MY_VAR)")
+        assert result == ParsedInput(name="MY_VAR", type="env")
+
+    def test_simple_file(self):
+        result = _parse_single_input("file(data)")
+        assert result == ParsedInput(name="data", type="file")
+
+    def test_stdin(self):
+        result = _parse_single_input("stdin")
+        assert result == ParsedInput(name="stdin", type="stdin")
+
+    def test_path_with_pattern(self):
+        result = _parse_single_input("path '*.txt'")
+        assert result == ParsedInput(name="*.txt", type="path")
+
+    def test_tuple_traditional(self):
+        result = _parse_single_input("tuple val(meta), path(reads)")
+        assert result is not None
+        assert result.type == "tuple"
+        assert result.name == "val(meta), path(reads)"
+
+    def test_tuple_multiple_paths(self):
+        result = _parse_single_input("tuple val(meta), path(reads), path(index)")
+        assert result is not None
+        assert result.type == "tuple"
+        assert result.name == "val(meta), path(reads), path(index)"
+
+    # Typed input syntax tests
+
+    def test_typed_tuple_two_elements(self):
+        """Typed tuple: (meta, bam): Tuple<Map, Path>"""
+        result = _parse_single_input("(meta, bam): Tuple<Map, Path>")
+        assert result is not None
+        assert result.type == "tuple"
+        assert result.name == "val(meta), path(bam)"
+        assert result.qualifier == "Tuple<Map, Path>"
+
+    def test_typed_tuple_three_elements(self):
+        """Typed tuple: (meta, bam, txt): Tuple<Map, Path, Path>"""
+        result = _parse_single_input("(meta, bam, txt): Tuple<Map, Path, Path>")
+        assert result is not None
+        assert result.type == "tuple"
+        assert result.name == "val(meta), path(bam), path(txt)"
+        assert result.qualifier == "Tuple<Map, Path, Path>"
+
+    def test_typed_tuple_all_vals(self):
+        """Typed tuple with all value types."""
+        result = _parse_single_input("(name, count): Tuple<String, Integer>")
+        assert result is not None
+        assert result.type == "tuple"
+        assert result.name == "val(name), val(count)"
+        assert result.qualifier == "Tuple<String, Integer>"
+
+    def test_typed_simple_integer(self):
+        """Simple typed input: x: Integer"""
+        result = _parse_single_input("x: Integer")
+        assert result is not None
+        assert result.type == "val"
+        assert result.name == "x"
+        assert result.qualifier == "Integer"
+
+    def test_typed_simple_path(self):
+        """Simple typed input: bam: Path"""
+        result = _parse_single_input("bam: Path")
+        assert result is not None
+        assert result.type == "path"
+        assert result.name == "bam"
+        assert result.qualifier == "Path"
+
+    def test_typed_simple_string(self):
+        """Simple typed input: name: String"""
+        result = _parse_single_input("name: String")
+        assert result is not None
+        assert result.type == "val"
+        assert result.name == "name"
+        assert result.qualifier == "String"
+
+    def test_typed_simple_map(self):
+        """Simple typed input: meta: Map"""
+        result = _parse_single_input("meta: Map")
+        assert result is not None
+        assert result.type == "val"
+        assert result.name == "meta"
+        assert result.qualifier == "Map"
+
+    def test_typed_simple_file(self):
+        """Simple typed input: data: File"""
+        result = _parse_single_input("data: File")
+        assert result is not None
+        assert result.type == "path"
+        assert result.name == "data"
+        assert result.qualifier == "File"
+
+    def test_each_qualifier_not_mismatched_as_typed(self):
+        """Traditional 'each' qualifier must not be parsed as typed input."""
+        # 'each' followed by a colon-like pattern should not match typed simple
+        result = _parse_single_input("each val(x)")
+        # 'each val(x)' is not currently handled - should return None rather than misparsing
+        assert result is None
+
+    def test_typed_tuple_mismatched_counts(self):
+        """Typed tuple with more names than types falls back to val() for extras."""
+        result = _parse_single_input("(a, b, c): Tuple<Map, Path>")
+        assert result is not None
+        assert result.type == "tuple"
+        # 'a' -> val(a), 'b' -> path(b), 'c' -> val(c) (fallback)
+        assert result.name == "val(a), path(b), val(c)"
+        assert result.qualifier == "Tuple<Map, Path>"
+
+
+class TestTypedToQualifier:
+    """Tests for _typed_to_qualifier."""
+
+    def test_path_type(self):
+        assert _typed_to_qualifier("Path") == "path"
+
+    def test_file_type(self):
+        assert _typed_to_qualifier("File") == "path"
+
+    def test_map_type(self):
+        assert _typed_to_qualifier("Map") == "val"
+
+    def test_integer_type(self):
+        assert _typed_to_qualifier("Integer") == "val"
+
+    def test_string_type(self):
+        assert _typed_to_qualifier("String") == "val"
+
+    def test_boolean_type(self):
+        assert _typed_to_qualifier("Boolean") == "val"
+
+
+class TestParseSingleOutput:
+    """Tests for _parse_single_output."""
+
+    def test_empty_line(self):
+        assert _parse_single_output("") is None
+        assert _parse_single_output("   ") is None
+
+    def test_simple_path_with_emit(self):
+        result = _parse_single_output('path "versions.yml", emit: versions')
+        assert result is not None
+        assert result.type == "path"
+        assert result.name == "versions.yml"
+        assert result.emit == "versions"
+
+    def test_tuple_with_emit(self):
+        result = _parse_single_output('tuple val(meta), path("*.html"), emit: html')
+        assert result is not None
+        assert result.type == "tuple"
+        assert result.name == 'val(meta), path("*.html")'
+        assert result.emit == "html"
+
+    def test_stdout(self):
+        result = _parse_single_output("stdout")
+        assert result is not None
+        assert result.type == "stdout"
+
+    def test_optional_output(self):
+        result = _parse_single_output('path "*.log", emit: log, optional: true')
+        assert result is not None
+        assert result.optional is True
+
+    # Named assignment output tests (typed syntax)
+
+    def test_named_tuple_output(self):
+        """Named assignment: txt = tuple(meta, file("*_svpileup.txt"))"""
+        result = _parse_single_output('txt = tuple(meta, file("*_svpileup.txt"))')
+        assert result is not None
+        assert result.type == "tuple"
+        assert result.emit == "txt"
+        assert 'file("*_svpileup.txt")' in result.name
+
+    def test_named_tuple_with_two_files(self):
+        """Named assignment: bam = tuple(meta, file("*_sorted.bam"))"""
+        result = _parse_single_output('bam = tuple(meta, file("*_sorted.bam"))')
+        assert result is not None
+        assert result.type == "tuple"
+        assert result.emit == "bam"
+
+    def test_named_simple_file(self):
+        """Named assignment: report = file("*.html")"""
+        result = _parse_single_output('report = file("*.html")')
+        assert result is not None
+        assert result.type == "file"
+        assert result.name == "*.html"
+        assert result.emit == "report"
+
+    def test_named_simple_path(self):
+        """Named assignment: versions = path("versions.yml")"""
+        result = _parse_single_output('versions = path("versions.yml")')
+        assert result is not None
+        assert result.type == "path"
+        assert result.name == "versions.yml"
+        assert result.emit == "versions"
+
+    def test_named_val(self):
+        """Named assignment: count = val(total)"""
+        result = _parse_single_output("count = val(total)")
+        assert result is not None
+        assert result.type == "val"
+        assert result.name == "total"
+        assert result.emit == "count"
+
+    def test_topic_publish_skipped(self):
+        """Topic publish lines should be skipped."""
+        assert _parse_single_output(">> 'sample_outputs'") is None
+        assert _parse_single_output('>> "my_topic"') is None
+
+
+class TestParseNamedOutput:
+    """Tests for _parse_named_output."""
+
+    def test_tuple_with_file(self):
+        result = _parse_named_output("txt", 'tuple(meta, file("*_svpileup.txt"))')
+        assert result.type == "tuple"
+        assert result.emit == "txt"
+        assert "file" in result.name
+
+    def test_tuple_with_multiple_components(self):
+        result = _parse_named_output("out", 'tuple(meta, file("*.bam"), file("*.bai"))')
+        assert result.type == "tuple"
+        assert result.emit == "out"
+
+    def test_tuple_plain_names(self):
+        result = _parse_named_output("result", "tuple(meta, data)")
+        assert result.type == "tuple"
+        assert result.emit == "result"
+        assert result.name == "val(meta), val(data)"
+
+    def test_simple_file(self):
+        result = _parse_named_output("report", 'file("report.html")')
+        assert result.type == "file"
+        assert result.emit == "report"
+        assert result.name == "report.html"
+
+    def test_simple_path(self):
+        result = _parse_named_output("versions", 'path("versions.yml")')
+        assert result.type == "path"
+        assert result.emit == "versions"
+        assert result.name == "versions.yml"
+
+    def test_fallback(self):
+        result = _parse_named_output("x", "some_expression")
+        assert result.type == "val"
+        assert result.emit == "x"
+        assert result.name == "some_expression"
+
+
+class TestParseProcessHover:
+    """Tests for parse_process_hover."""
+
+    def test_traditional_process(self):
+        """Parse a traditional DSL2 process definition."""
+        hover = """```nextflow
+process FASTQC {
+  input:
+  tuple val(meta), path(reads)
+
+  output:
+  tuple val(meta), path("*.html"), emit: html
+  path "versions.yml", emit: versions
+}
+```"""
+        result = parse_process_hover(hover)
+        assert result is not None
+        assert result.name == "FASTQC"
+        assert len(result.inputs) == 1
+        assert result.inputs[0].type == "tuple"
+        assert len(result.outputs) == 2
+        assert result.outputs[0].emit == "html"
+        assert result.outputs[1].emit == "versions"
+
+    def test_typed_process(self):
+        """Parse a typed process definition (Nextflow typed syntax)."""
+        hover = """```nextflow
+process SV_PILEUP {
+  input:
+  (meta, bam): Tuple<Map, Path>
+
+  output:
+  txt = tuple(meta, file("*_svpileup.txt"))
+  bam = tuple(meta, file("*_svpileup.bam"))
+}
+```"""
+        result = parse_process_hover(hover)
+        assert result is not None
+        assert result.name == "SV_PILEUP"
+        assert len(result.inputs) == 1
+        assert result.inputs[0].type == "tuple"
+        assert result.inputs[0].name == "val(meta), path(bam)"
+        assert result.inputs[0].qualifier == "Tuple<Map, Path>"
+        assert len(result.outputs) == 2
+        assert result.outputs[0].emit == "txt"
+        assert result.outputs[0].type == "tuple"
+        assert result.outputs[1].emit == "bam"
+        assert result.outputs[1].type == "tuple"
+
+    def test_typed_process_three_inputs(self):
+        """Parse typed process with 3-element tuple input."""
+        hover = """```nextflow
+process AGGREGATE {
+  input:
+  (meta, bam, txt): Tuple<Map, Path, Path>
+
+  output:
+  txt = tuple(meta, file("*_aggregate.txt"))
+}
+```"""
+        result = parse_process_hover(hover)
+        assert result is not None
+        assert result.name == "AGGREGATE"
+        assert len(result.inputs) == 1
+        assert result.inputs[0].name == "val(meta), path(bam), path(txt)"
+        assert len(result.outputs) == 1
+        assert result.outputs[0].emit == "txt"
+
+    def test_typed_process_with_topic_section(self):
+        """Topic section should not interfere with output parsing."""
+        hover = """```nextflow
+process MY_PROC {
+  input:
+  (meta, bam): Tuple<Map, Path>
+
+  output:
+  txt = tuple(meta, file("*.txt"))
+
+  topic:
+  >> 'sample_outputs'
+}
+```"""
+        result = parse_process_hover(hover)
+        assert result is not None
+        assert len(result.inputs) == 1
+        assert len(result.outputs) == 1
+        assert result.outputs[0].emit == "txt"
+
+    def test_mixed_typed_and_traditional_outputs(self):
+        """Process with both named assignment and traditional output syntax."""
+        hover = """```nextflow
+process MIXED {
+  input:
+  val(x)
+
+  output:
+  txt = file("output.txt")
+  path "versions.yml", emit: versions
+}
+```"""
+        result = parse_process_hover(hover)
+        assert result is not None
+        assert len(result.outputs) == 2
+        assert result.outputs[0].emit == "txt"
+        assert result.outputs[0].type == "file"
+        assert result.outputs[1].emit == "versions"
+
+    def test_typed_simple_inputs(self):
+        """Process with simple typed inputs."""
+        hover = """```nextflow
+process SIMPLE_TYPED {
+  input:
+  x: Integer
+  bam: Path
+
+  output:
+  result = val(x)
+}
+```"""
+        result = parse_process_hover(hover)
+        assert result is not None
+        assert len(result.inputs) == 2
+        assert result.inputs[0].name == "x"
+        assert result.inputs[0].type == "val"
+        assert result.inputs[0].qualifier == "Integer"
+        assert result.inputs[1].name == "bam"
+        assert result.inputs[1].type == "path"
+        assert result.inputs[1].qualifier == "Path"
+
+    def test_no_code_block(self):
+        """Handle hover text without code fences."""
+        result = parse_process_hover("just some text")
+        assert result is None
+
+    def test_empty_process(self):
+        """Process with no inputs or outputs."""
+        hover = """```nextflow
+process EMPTY {
+  script:
+  echo "hello"
+}
+```"""
+        result = parse_process_hover(hover)
+        assert result is not None
+        assert result.name == "EMPTY"
+        assert len(result.inputs) == 0
+        assert len(result.outputs) == 0
+
+    def test_topic_in_output_block_skipped(self):
+        """Topic publish lines within output block should be skipped."""
+        hover = """```nextflow
+process WITH_TOPIC {
+  output:
+  txt = file("out.txt")
+  >> 'my_topic'
+}
+```"""
+        result = parse_process_hover(hover)
+        assert result is not None
+        # Only the file output, not the topic line
+        assert len(result.outputs) == 1
+        assert result.outputs[0].emit == "txt"
+
+
+class TestParseWorkflowHover:
+    """Tests for parse_workflow_hover."""
+
+    def test_workflow_with_takes_and_emits(self):
+        hover = """```nextflow
+workflow MAIN {
+  take:
+  reads
+  genome
+
+  emit:
+  bam = aligned
+  vcf = variants
+}
+```"""
+        result = parse_workflow_hover(hover)
+        assert result is not None
+        assert result.name == "MAIN"
+        assert result.takes == ["reads", "genome"]
+        assert result.emits == ["bam", "vcf"]
+
+    def test_empty_workflow(self):
+        hover = """```nextflow
+workflow EMPTY {
+}
+```"""
+        result = parse_workflow_hover(hover)
+        assert result is not None
+        assert result.name == "EMPTY"
+        assert result.takes == []
+        assert result.emits == []

From 66d57abbe41be2464ea6157d36bdba19f44e7a29 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Tue, 3 Mar 2026 15:48:10 +0100
Subject: [PATCH 2/9] Fix bare typed outputs and ? type from LSP hover

The Nextflow LSP returns bare emit names (e.g. 'txt', 'bam') as
outputs for typed processes, rather than qualified declarations.
Add handling for these bare identifier outputs in _parse_single_output.

Also add tests for ? type in typed tuples (LSP representation of
Map type) and integration tests matching real LSP hover output from
nf-fgsv pipeline.

Verified against fulcrumgenomics/nf-fgsv: all 4 processes now
correctly show both inputs and outputs.
---
 src/nf_docs/nf_parser.py | 12 +++++-
 tests/test_nf_parser.py  | 83 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 93 insertions(+), 2 deletions(-)

diff --git a/src/nf_docs/nf_parser.py b/src/nf_docs/nf_parser.py
index 1f03591..3cdeffc 100644
--- a/src/nf_docs/nf_parser.py
+++ b/src/nf_docs/nf_parser.py
@@ -203,8 +203,10 @@ def _parse_single_input(line: str) -> ParsedInput | None:
 def _typed_to_qualifier(type_name: str) -> str:
     """Map a Nextflow type annotation to a traditional qualifier name.
 
+    The Nextflow LSP may represent unknown or unresolved types as ``?``.
+
     Args:
-        type_name: The type annotation (e.g. ``Path``, ``Map``, ``Integer``).
+        type_name: The type annotation (e.g. ``Path``, ``Map``, ``Integer``, ``?``).
 
     Returns:
         The corresponding traditional qualifier (``val``, ``path``, etc.).
@@ -212,7 +214,7 @@ def _typed_to_qualifier(type_name: str) -> str:
     path_types = {"Path", "File"}
     if type_name in path_types:
         return "path"
-    # Everything else maps to val (Map, Integer, String, Boolean, etc.)
+    # Everything else maps to val (Map, Integer, String, Boolean, ?, etc.)
     return "val"
 
 
@@ -286,6 +288,12 @@ def _parse_single_output(line: str) -> ParsedOutput | None:
         )
         return ParsedOutput(name=name, type=output_type, emit=emit_name, optional=optional)
 
+    # Handle bare emit names from typed outputs (LSP returns just the name, e.g. "txt", "bam")
+    bare_name_match = re.match(r"(\w+)$", line)
+    if bare_name_match:
+        name = bare_name_match.group(1)
+        return ParsedOutput(name=name, type="", emit=name)
+
     return None
 
 
diff --git a/tests/test_nf_parser.py b/tests/test_nf_parser.py
index 07af079..19bfc53 100644
--- a/tests/test_nf_parser.py
+++ b/tests/test_nf_parser.py
@@ -120,6 +120,22 @@ def test_typed_simple_file(self):
         assert result.name == "data"
         assert result.qualifier == "File"
 
+    def test_typed_tuple_with_question_mark_type(self):
+        """Typed tuple with ? (unresolved) type from LSP: (meta, bam): Tuple<?, Path>"""
+        result = _parse_single_input("(meta, bam): Tuple<?, Path>")
+        assert result is not None
+        assert result.type == "tuple"
+        assert result.name == "val(meta), path(bam)"
+        assert result.qualifier == "Tuple<?, Path>"
+
+    def test_typed_tuple_three_with_question_mark(self):
+        """Typed 3-tuple with ? type: (meta, bam, txt): Tuple<?, Path, Path>"""
+        result = _parse_single_input("(meta, bam, txt): Tuple<?, Path, Path>")
+        assert result is not None
+        assert result.type == "tuple"
+        assert result.name == "val(meta), path(bam), path(txt)"
+        assert result.qualifier == "Tuple<?, Path, Path>"
+
     def test_each_qualifier_not_mismatched_as_typed(self):
         """Traditional 'each' qualifier must not be parsed as typed input."""
         # 'each' followed by a colon-like pattern should not match typed simple
@@ -231,6 +247,28 @@ def test_named_val(self):
         assert result.name == "total"
         assert result.emit == "count"
 
+    def test_bare_emit_name(self):
+        """Bare identifier output from typed syntax LSP hover (e.g. just 'txt')."""
+        result = _parse_single_output("txt")
+        assert result is not None
+        assert result.name == "txt"
+        assert result.emit == "txt"
+        assert result.type == ""
+
+    def test_bare_emit_name_bam(self):
+        """Bare identifier output: bam."""
+        result = _parse_single_output("bam")
+        assert result is not None
+        assert result.name == "bam"
+        assert result.emit == "bam"
+
+    def test_bare_emit_name_bedpe(self):
+        """Bare identifier output: bedpe."""
+        result = _parse_single_output("bedpe")
+        assert result is not None
+        assert result.name == "bedpe"
+        assert result.emit == "bedpe"
+
     def test_topic_publish_skipped(self):
         """Topic publish lines should be skipped."""
         assert _parse_single_output(">> 'sample_outputs'") is None
@@ -439,6 +477,51 @@ def test_topic_in_output_block_skipped(self):
         assert len(result.outputs) == 1
         assert result.outputs[0].emit == "txt"
 
+    def test_typed_process_with_bare_outputs(self):
+        """Real LSP hover for a typed process with bare emit names as outputs."""
+        hover = """```nextflow
+process SV_PILEUP {
+  input:
+  (meta, bam): Tuple<?, Path>
+
+  output:
+  txt
+  bam
+}
+```"""
+        result = parse_process_hover(hover)
+        assert result is not None
+        assert result.name == "SV_PILEUP"
+        # Input: typed tuple with ? type
+        assert len(result.inputs) == 1
+        assert result.inputs[0].type == "tuple"
+        assert result.inputs[0].name == "val(meta), path(bam)"
+        assert result.inputs[0].qualifier == "Tuple<?, Path>"
+        # Outputs: bare emit names
+        assert len(result.outputs) == 2
+        assert result.outputs[0].name == "txt"
+        assert result.outputs[0].emit == "txt"
+        assert result.outputs[1].name == "bam"
+        assert result.outputs[1].emit == "bam"
+
+    def test_typed_process_three_inputs_bare_output(self):
+        """Real LSP hover for typed process with 3-element tuple and bare output."""
+        hover = """```nextflow
+process AGGREGATE_SV_PILEUP {
+  input:
+  (meta, bam, txt): Tuple<?, Path, Path>
+
+  output:
+  txt
+}
+```"""
+        result = parse_process_hover(hover)
+        assert result is not None
+        assert len(result.inputs) == 1
+        assert result.inputs[0].name == "val(meta), path(bam), path(txt)"
+        assert len(result.outputs) == 1
+        assert result.outputs[0].emit == "txt"
+
 
 class TestParseWorkflowHover:
     """Tests for parse_workflow_hover."""

From f747d3b2e6860bb97f59907e7ff93a2469b4f75a Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Tue, 3 Mar 2026 15:57:17 +0100
Subject: [PATCH 3/9] Enrich bare typed outputs from .nf source files

When the Nextflow LSP returns only bare emit names for typed process
outputs (e.g. 'txt', 'bam'), read the actual .nf source file to get
the full output declarations (e.g. txt = tuple(meta, file("*.txt"))).

- Add enrich_outputs_from_source() in nf_parser.py to parse the
  source output block and replace bare outputs with rich declarations
- Add _parse_tuple_components() to handle mixed qualified/bare tuple
  elements (e.g. tuple(meta, file("*.txt")) -> val(meta), file(...))
- Call enrichment from extractor when bare outputs are detected
- Add 6 tests for the enrichment function

Verified against nf-fgsv: outputs now show val(meta), file("*") with
type=tuple and emit names, matching the quality of typed inputs.
---
 src/nf_docs/extractor.py |  22 ++++--
 src/nf_docs/nf_parser.py | 144 ++++++++++++++++++++++++++++++++++++---
 tests/test_nf_parser.py  | 107 +++++++++++++++++++++++++++++
 3 files changed, 258 insertions(+), 15 deletions(-)

diff --git a/src/nf_docs/extractor.py b/src/nf_docs/extractor.py
index fed260c..301a7b8 100644
--- a/src/nf_docs/extractor.py
+++ b/src/nf_docs/extractor.py
@@ -38,7 +38,7 @@
     WorkflowInput,
     WorkflowOutput,
 )
-from nf_docs.nf_parser import parse_process_hover, parse_workflow_hover
+from nf_docs.nf_parser import enrich_outputs_from_source, parse_process_hover, parse_workflow_hover
 from nf_docs.progress import (
     ExtractionPhase,
     ProgressCallbackType,
@@ -586,7 +586,14 @@ def _process_symbol(
         # Determine what kind of symbol this is based on parsed type or LSP kind
         if symbol_type == "process" or kind == SymbolKind.METHOD:
             process = self._create_process_from_signature(
-                name, signature, docstring, relative_path, line + 1, end_line + 1, source_url
+                name,
+                signature,
+                docstring,
+                relative_path,
+                line + 1,
+                end_line + 1,
+                source_url,
+                source_path=file_path,
             )
             if process and not any(p.name == process.name for p in pipeline.processes):
                 # Apply meta.yml data if available (for modules)
@@ -638,11 +645,12 @@ def _create_process_from_signature(
         line: int,
         end_line: int = 0,
         source_url: str = "",
+        source_path: Path | None = None,
     ) -> Process | None:
         """Create a Process by parsing the LSP signature."""
         process = Process(
             name=name,
-            docstring=docstring,  # Actual Groovydoc documentation
+            docstring=docstring,
             file=file_path,
             line=line,
             end_line=end_line,
@@ -660,11 +668,17 @@ def _create_process_from_signature(
         # }
         parsed = parse_process_hover(f"```nextflow\n{signature}\n```")
         if parsed:
+            # Enrich bare-name outputs from the source file when the LSP
+            # only returns emit names (common with typed Nextflow syntax)
+            outputs = parsed.outputs
+            if source_path and any(not o.type for o in outputs):
+                outputs = enrich_outputs_from_source(outputs, source_path, name)
+
             for inp in parsed.inputs:
                 process.inputs.append(
                     ProcessInput(name=inp.name, type=inp.type, qualifier=inp.qualifier)
                 )
-            for out in parsed.outputs:
+            for out in outputs:
                 process.outputs.append(ProcessOutput(name=out.name, type=out.type, emit=out.emit))
 
         return process
diff --git a/src/nf_docs/nf_parser.py b/src/nf_docs/nf_parser.py
index 3cdeffc..27bd5d1 100644
--- a/src/nf_docs/nf_parser.py
+++ b/src/nf_docs/nf_parser.py
@@ -5,13 +5,17 @@
 to extract inputs, outputs, and other metadata.
 """
 
+import logging
 import re
 from dataclasses import dataclass, field
+from pathlib import Path
 
 # Traditional Nextflow input qualifiers that should not be treated as typed variable names.
 # Used to prevent false matches like "each: sample" being parsed as typed input "each" of type "sample".
 _TRADITIONAL_QUALIFIERS = frozenset({"val", "path", "file", "env", "stdin", "tuple", "each"})
 
+logger = logging.getLogger(__name__)
+
 
 @dataclass
 class ParsedInput:
@@ -297,6 +301,46 @@ def _parse_single_output(line: str) -> ParsedOutput | None:
     return None
 
 
+def _parse_tuple_components(inner: str) -> list[str]:
+    """Parse the components inside a ``tuple(...)`` expression.
+
+    Handles mixed content where some elements are qualified
+    (``file("...")``, ``val(x)``, ``path("...")``) and others are bare
+    names (``meta``, ``bam``).  Bare names are wrapped as ``val(name)``.
+
+    Args:
+        inner: The content inside the outer ``tuple()`` parentheses,
+            e.g. ``'meta, file("*_svpileup.txt")'``.
+
+    Returns:
+        List of formatted component strings like ``["val(meta)", "file(\\"*_svpileup.txt\\")"]``.
+    """
+    parts: list[str] = []
+    # Match qualified components and their positions
+    qualifier_re = re.compile(r"(val|path|file|env)\s*\(([^)]+)\)")
+    last_end = 0
+
+    for m in qualifier_re.finditer(inner):
+        # Any text between the last match end and this match start may contain bare names
+        gap = inner[last_end : m.start()]
+        for bare in re.findall(r"\b(\w+)\b", gap):
+            parts.append(f"val({bare})")
+        parts.append(f"{m.group(1)}({m.group(2)})")
+        last_end = m.end()
+
+    # Handle any trailing bare names after the last qualified component
+    gap = inner[last_end:]
+    for bare in re.findall(r"\b(\w+)\b", gap):
+        parts.append(f"val({bare})")
+
+    # Fallback: if nothing was parsed, split by comma and wrap as val()
+    if not parts:
+        names = [n.strip() for n in inner.split(",")]
+        parts = [f"val({n})" for n in names if n]
+
+    return parts
+
+
 def _parse_named_output(emit_name: str, rhs: str) -> ParsedOutput:
     """Parse the right-hand side of a named output assignment.
 
@@ -319,17 +363,8 @@ def _parse_named_output(emit_name: str, rhs: str) -> ParsedOutput:
     tuple_match = re.match(r"tuple\s*\((.+)\)\s*$", rhs)
     if tuple_match:
         inner = tuple_match.group(1)
-        # Extract typed components: file("..."), val(...), path("...")
-        components = re.findall(r"(val|path|file|env)\s*\(([^)]+)\)", inner)
-        if components:
-            parts = []
-            for comp_type, comp_name in components:
-                parts.append(f"{comp_type}({comp_name})")
-            name = ", ".join(parts)
-        else:
-            # Plain names: tuple(meta, bam)
-            names = [n.strip() for n in inner.split(",")]
-            name = ", ".join(f"val({n})" for n in names)
+        parts = _parse_tuple_components(inner)
+        name = ", ".join(parts)
         return ParsedOutput(name=name, type="tuple", emit=emit_name)
 
     # Handle simple: file("*.bam"), path("versions.yml"), val(x)
@@ -419,3 +454,90 @@ def is_code_block(text: str) -> bool:
             return True
 
     return False
+
+
+def enrich_outputs_from_source(
+    outputs: list[ParsedOutput],
+    source_path: Path,
+    process_name: str,
+) -> list[ParsedOutput]:
+    """Enrich bare-name outputs with full declarations parsed from the ``.nf`` source.
+
+    When the Nextflow LSP returns bare emit names for typed process outputs
+    (e.g. ``txt``, ``bam`` instead of ``txt = tuple(meta, file("*.txt"))``),
+    this function reads the actual source file and parses the named-assignment
+    output declarations to provide full type and component information.
+
+    If a bare output's emit name matches a named assignment in the source, the
+    bare output is replaced with the richer parsed version.  Outputs that are
+    already fully qualified (have a non-empty ``type``) are left untouched.
+
+    Args:
+        outputs: The outputs parsed from the LSP hover (may contain bare names).
+        source_path: Absolute path to the ``.nf`` source file.
+        process_name: Name of the process to locate in the source.
+
+    Returns:
+        A new list of ``ParsedOutput`` objects, enriched where possible.
+    """
+    # Only enrich if there are bare outputs (type is empty)
+    bare_outputs = [o for o in outputs if not o.type]
+    if not bare_outputs:
+        return outputs
+
+    try:
+        source = source_path.read_text(encoding="utf-8")
+    except OSError as e:
+        logger.debug(f"Could not read source file {source_path} for output enrichment: {e}")
+        return outputs
+
+    # Find the process block in source
+    proc_pattern = re.compile(rf"process\s+{re.escape(process_name)}\s*\{{", re.MULTILINE)
+    proc_match = proc_pattern.search(source)
+    if not proc_match:
+        logger.debug(f"Could not find process {process_name} in {source_path}")
+        return outputs
+
+    # Extract the process body (find matching closing brace)
+    proc_start = proc_match.start()
+    brace_depth = 0
+    proc_body = ""
+    for i in range(proc_match.end() - 1, len(source)):
+        if source[i] == "{":
+            brace_depth += 1
+        elif source[i] == "}":
+            brace_depth -= 1
+            if brace_depth == 0:
+                proc_body = source[proc_start : i + 1]
+                break
+
+    if not proc_body:
+        return outputs
+
+    # Extract the output section from the source process body
+    output_match = re.search(
+        r"output:\s*(.*?)(?:topic:|script:|shell:|exec:|when:|\})",
+        proc_body,
+        re.DOTALL,
+    )
+    if not output_match:
+        return outputs
+
+    # Parse the source output declarations
+    source_outputs = _parse_output_declarations(output_match.group(1))
+
+    # Build a lookup by emit name
+    source_by_emit: dict[str, ParsedOutput] = {}
+    for out in source_outputs:
+        if out.emit:
+            source_by_emit[out.emit] = out
+
+    # Replace bare outputs with enriched versions
+    enriched = []
+    for out in outputs:
+        if not out.type and out.emit in source_by_emit:
+            enriched.append(source_by_emit[out.emit])
+        else:
+            enriched.append(out)
+
+    return enriched
diff --git a/tests/test_nf_parser.py b/tests/test_nf_parser.py
index 19bfc53..9316477 100644
--- a/tests/test_nf_parser.py
+++ b/tests/test_nf_parser.py
@@ -1,11 +1,15 @@
 """Tests for the Nextflow code parser."""
 
+from pathlib import Path
+
 from nf_docs.nf_parser import (
     ParsedInput,
+    ParsedOutput,
     _parse_named_output,
     _parse_single_input,
     _parse_single_output,
     _typed_to_qualifier,
+    enrich_outputs_from_source,
     parse_process_hover,
     parse_workflow_hover,
 )
@@ -554,3 +558,106 @@ def test_empty_workflow(self):
         assert result.name == "EMPTY"
         assert result.takes == []
         assert result.emits == []
+
+
+class TestEnrichOutputsFromSource:
+    """Tests for enriching bare outputs with data from .nf source files."""
+
+    SV_PILEUP_SOURCE = """\
+process SV_PILEUP {
+    container "community.wave.seqera.io/library/fgsv:0.2.1"
+
+    input:
+    (meta, bam): Tuple<?, Path>
+
+    output:
+    txt = tuple(meta, file("*_svpileup.txt"))
+    bam = tuple(meta, file("*_svpileup.bam"))
+
+    topic:
+    tuple(meta, file("*_svpileup.txt")) >> 'sample_outputs'
+
+    script:
+    def prefix = "${meta.id}"
+    \"""
+    fgsv SvPileup --input ${bam} --output ${prefix}_svpileup
+    \"""
+}
+"""
+
+    def test_bare_outputs_enriched(self, tmp_path: Path):
+        """Bare emit names are replaced with full declarations from source."""
+        source_file = tmp_path / "sv_pileup.nf"
+        source_file.write_text(self.SV_PILEUP_SOURCE)
+
+        bare_outputs = [
+            ParsedOutput(name="txt", type="", emit="txt"),
+            ParsedOutput(name="bam", type="", emit="bam"),
+        ]
+        result = enrich_outputs_from_source(bare_outputs, source_file, "SV_PILEUP")
+
+        assert len(result) == 2
+        assert result[0].emit == "txt"
+        assert result[0].type == "tuple"
+        assert "file(" in result[0].name
+        assert result[1].emit == "bam"
+        assert result[1].type == "tuple"
+        assert "file(" in result[1].name
+
+    def test_already_qualified_outputs_not_changed(self, tmp_path: Path):
+        """Outputs that already have a type are left untouched."""
+        source_file = tmp_path / "sv_pileup.nf"
+        source_file.write_text(self.SV_PILEUP_SOURCE)
+
+        qualified_outputs = [
+            ParsedOutput(name="val(meta), path(*.html)", type="tuple", emit="html"),
+        ]
+        result = enrich_outputs_from_source(qualified_outputs, source_file, "SV_PILEUP")
+
+        assert len(result) == 1
+        assert result[0] is qualified_outputs[0]  # same object, unchanged
+
+    def test_missing_source_file_returns_originals(self, tmp_path: Path):
+        """If the source file doesn't exist, return outputs unchanged."""
+        bare_outputs = [ParsedOutput(name="txt", type="", emit="txt")]
+        result = enrich_outputs_from_source(bare_outputs, tmp_path / "nonexistent.nf", "SV_PILEUP")
+        assert result is bare_outputs
+
+    def test_process_not_found_returns_originals(self, tmp_path: Path):
+        """If the process name isn't in the source, return outputs unchanged."""
+        source_file = tmp_path / "other.nf"
+        source_file.write_text("process OTHER_PROC {\n  output:\n  x = val(1)\n}\n")
+
+        bare_outputs = [ParsedOutput(name="txt", type="", emit="txt")]
+        result = enrich_outputs_from_source(bare_outputs, source_file, "SV_PILEUP")
+        assert result is bare_outputs
+
+    def test_partial_match_enriches_only_matching(self, tmp_path: Path):
+        """Only bare outputs whose emit matches a source declaration are enriched."""
+        source_file = tmp_path / "sv_pileup.nf"
+        source_file.write_text(self.SV_PILEUP_SOURCE)
+
+        outputs = [
+            ParsedOutput(name="txt", type="", emit="txt"),
+            ParsedOutput(name="unknown", type="", emit="unknown"),
+        ]
+        result = enrich_outputs_from_source(outputs, source_file, "SV_PILEUP")
+
+        assert result[0].type == "tuple"  # enriched
+        assert result[0].emit == "txt"
+        assert result[1].type == ""  # not found in source, unchanged
+        assert result[1].emit == "unknown"
+
+    def test_simple_named_output(self, tmp_path: Path):
+        """Named simple output: versions = path("versions.yml")."""
+        source_file = tmp_path / "proc.nf"
+        source_file.write_text(
+            'process SIMPLE {\n  output:\n  versions = path("versions.yml")\n\n  script:\n  ""\n}\n'
+        )
+
+        bare_outputs = [ParsedOutput(name="versions", type="", emit="versions")]
+        result = enrich_outputs_from_source(bare_outputs, source_file, "SIMPLE")
+
+        assert result[0].emit == "versions"
+        assert result[0].type == "path"
+        assert result[0].name == "versions.yml"

From 31c9d053670832dea6133b04d699268134f74408 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Tue, 3 Mar 2026 16:23:40 +0100
Subject: [PATCH 4/9] Fix params not showing: prefix README heading IDs to
 avoid collisions

README headings like '## Inputs' generated id='inputs', colliding
with the page-level section id='inputs' used for Parameters navigation.
When JavaScript called getElementById('inputs'), it found the README
heading first (earlier in DOM), leaving the Parameters section hidden.

Fix by prefixing all README heading IDs with 'readme-' (e.g.
'readme-inputs'), keeping section IDs intact for navigation.
---
 src/nf_docs/renderers/html.py | 42 +++++++++++++++++++++++++----------
 1 file changed, 30 insertions(+), 12 deletions(-)

diff --git a/src/nf_docs/renderers/html.py b/src/nf_docs/renderers/html.py
index 047ecd9..cd36de8 100644
--- a/src/nf_docs/renderers/html.py
+++ b/src/nf_docs/renderers/html.py
@@ -254,12 +254,20 @@ def _slugify(text: str) -> str:
     return slug.strip("-")
 
 
-def _add_heading_anchors(html: str) -> str:
-    """
-    Add IDs and anchor links to headings in HTML.
+def _add_heading_anchors(html: str, prefix: str = "") -> str:
+    """Add IDs and anchor links to headings in HTML.
+
+    Transforms ``<h1>Title</h1>`` to::
+
+        <h1 id="title" class="heading-anchor">
+          Title<a href="#title" class="paragraph-link">¶</a>
+        </h1>
 
-    Transforms <h1>Title</h1> to:
-    <h1 id="title" class="heading-anchor">Title<a href="#title" class="paragraph-link">¶</a></h1>
+    Args:
+        html: The HTML string to process.
+        prefix: Optional prefix for generated IDs (e.g. ``"readme-"``).
+            Used to avoid collisions with page-level section IDs when
+            the headings come from embedded content like a README.
     """
     heading_pattern = re.compile(r"<(h[1-6])>(.+?)</\1>", re.IGNORECASE | re.DOTALL)
 
@@ -271,7 +279,7 @@ def replace_heading(match: re.Match[str]) -> str:
 
         # Extract text content for the slug (strip any HTML tags)
         text_content = re.sub(r"<[^>]+>", "", content)
-        slug = _slugify(text_content)
+        slug = f"{prefix}{_slugify(text_content)}"
 
         # Handle duplicate IDs by appending a number
         if slug in seen_ids:
@@ -289,12 +297,18 @@ def replace_heading(match: re.Match[str]) -> str:
     return heading_pattern.sub(replace_heading, html)
 
 
-def md_to_html(text: str | None, add_anchors: bool = False) -> Markup:
+def md_to_html(
+    text: str | None,
+    add_anchors: bool = False,
+    heading_id_prefix: str = "",
+) -> Markup:
     """Convert markdown text to HTML, safe for Jinja templates.
 
     Args:
-        text: Markdown text to convert
-        add_anchors: If True, add IDs and anchor links to headings
+        text: Markdown text to convert.
+        add_anchors: If True, add IDs and anchor links to headings.
+        heading_id_prefix: Prefix for heading IDs (e.g. ``"readme-"``).
+            Only used when *add_anchors* is True.
     """
     if not text:
         return Markup("")
@@ -321,13 +335,17 @@ def md_to_html(text: str | None, add_anchors: bool = False) -> Markup:
     html = _process_github_alerts(html)
     # Optionally add heading anchors
     if add_anchors:
-        html = _add_heading_anchors(html)
+        html = _add_heading_anchors(html, prefix=heading_id_prefix)
     return Markup(html)
 
 
 def md_to_html_with_anchors(text: str | None) -> Markup:
-    """Convert markdown text to HTML with heading anchors."""
-    return md_to_html(text, add_anchors=True)
+    """Convert markdown text to HTML with heading anchors.
+
+    README heading IDs are prefixed with ``readme-`` to avoid collisions
+    with page-level section IDs (e.g. ``inputs``, ``processes``).
+    """
+    return md_to_html(text, add_anchors=True, heading_id_prefix="readme-")
 
 
 def add_word_breaks(text: str | None) -> Markup:

From 3e6b1cf6059ba40cfff9ecf8118003fabfe0890e Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Tue, 3 Mar 2026 16:28:17 +0100
Subject: [PATCH 5/9] Show pattern restriction in HTML parameter cards

The pattern field from nextflow_schema.json was already included in
JSON, YAML, and Markdown output but was missing from the HTML template.
Add it after the enum block in the parameter card.
---
 src/nf_docs/templates/html.html | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/nf_docs/templates/html.html b/src/nf_docs/templates/html.html
index f483d52..48f023b 100644
--- a/src/nf_docs/templates/html.html
+++ b/src/nf_docs/templates/html.html
@@ -1506,6 +1506,13 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">Pipeline Inputs</h1>
               <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm">{{ val }}</code>
               {% if not loop.last %}, {% endif %} {% endfor %}
             </p>
+            {% endif %} {% if inp.pattern %}
+            <p class="mt-2">
+              <strong>Pattern:</strong>
+              <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                >{{ inp.pattern }}</code
+              >
+            </p>
             {% endif %}
           </div>
           {% endfor %} {% endfor %}

From f46930a11af23bba7d1371b6b69ceadd28ff55c2 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Tue, 3 Mar 2026 18:12:02 +0100
Subject: [PATCH 6/9] Apply Groovydoc @param/@return descriptions to process
 inputs/outputs

- Parse @param and @return tags from LSP hover and apply descriptions
  to matching ProcessInput/ProcessOutput objects
- Support named @return tags (@return txt Description) so each output
  gets its own description instead of sharing a single _return key
- Fall back to reading Groovydoc directly from .nf source files when
  the LSP returns no param docs (common with typed processes)
- Support both @param/@return and Inputs:/Outputs: bullet-list formats
- Handle Groovydoc not immediately adjacent to process declaration
  (e.g. nextflow.preview.types = true between comment and process)
- Render all LSP-sourced descriptions through |markdown filter in HTML
  (consistent with meta.yml descriptions)
- Move pattern field from a separate block to an inline yellow badge
  in the parameter card, with dark mode support

Adds 8 tests for Groovydoc parsing and param description matching.
---
 src/nf_docs/extractor.py           | 241 +++++++++++++++++++++++++++--
 src/nf_docs/lsp_client.py          |  17 +-
 src/nf_docs/templates/html.html    |  47 ++++--
 src/nf_docs/templates/tailwind.css |   2 +-
 tests/test_extractor.py            | 122 +++++++++++++++
 5 files changed, 401 insertions(+), 28 deletions(-)

diff --git a/src/nf_docs/extractor.py b/src/nf_docs/extractor.py
index 301a7b8..4fdf601 100644
--- a/src/nf_docs/extractor.py
+++ b/src/nf_docs/extractor.py
@@ -594,6 +594,7 @@ def _process_symbol(
                 end_line + 1,
                 source_url,
                 source_path=file_path,
+                param_docs=param_docs,
             )
             if process and not any(p.name == process.name for p in pipeline.processes):
                 # Apply meta.yml data if available (for modules)
@@ -646,8 +647,28 @@ def _create_process_from_signature(
         end_line: int = 0,
         source_url: str = "",
         source_path: Path | None = None,
+        param_docs: dict[str, str] | None = None,
     ) -> Process | None:
-        """Create a Process by parsing the LSP signature."""
+        """Create a Process by parsing the LSP signature.
+
+        When the LSP hover includes Groovydoc ``@param`` / ``@return`` tags,
+        their descriptions are applied to the matching inputs and outputs.
+        If the LSP returns no docstring (common with typed Nextflow syntax),
+        the Groovydoc is parsed directly from the ``.nf`` source file.
+        """
+        if param_docs is None:
+            param_docs = {}
+
+        # If the LSP returned no param docs, try to parse them from the source file.
+        # The LSP may return the free-text docstring but strip @param/@return tags,
+        # or (for typed processes) return no docstring at all.
+        if source_path and not param_docs:
+            source_docstring, source_params = _parse_groovydoc_from_source(source_path, name)
+            if source_params:
+                param_docs = source_params
+            if not docstring and source_docstring:
+                docstring = source_docstring
+
         process = Process(
             name=name,
             docstring=docstring,
@@ -658,14 +679,6 @@ def _create_process_from_signature(
         )
 
         # Use the nf_parser to extract inputs/outputs from the signature
-        # The signature is in the format:
-        # process NAME {
-        #   input:
-        #   tuple val(meta), path(reads)
-        #
-        #   output:
-        #   tuple val(meta), path("*.html"), emit: html
-        # }
         parsed = parse_process_hover(f"```nextflow\n{signature}\n```")
         if parsed:
             # Enrich bare-name outputs from the source file when the LSP
@@ -675,11 +688,29 @@ def _create_process_from_signature(
                 outputs = enrich_outputs_from_source(outputs, source_path, name)
 
             for inp in parsed.inputs:
+                # Look up @param description by matching input component names
+                description = _find_param_description(inp.name, param_docs)
                 process.inputs.append(
-                    ProcessInput(name=inp.name, type=inp.type, qualifier=inp.qualifier)
+                    ProcessInput(
+                        name=inp.name,
+                        type=inp.type,
+                        qualifier=inp.qualifier,
+                        description=description,
+                    )
                 )
             for out in outputs:
-                process.outputs.append(ProcessOutput(name=out.name, type=out.type, emit=out.emit))
+                # Look up @return description by emit name
+                description = param_docs.get(f"_return_{out.emit}", "")
+                if not description:
+                    description = param_docs.get("_return", "")
+                process.outputs.append(
+                    ProcessOutput(
+                        name=out.name,
+                        type=out.type,
+                        emit=out.emit,
+                        description=description,
+                    )
+                )
 
         return process
 
@@ -773,3 +804,191 @@ def _create_function_from_signature(
                         )
 
         return function
+
+
+def _find_param_description(input_name: str, param_docs: dict[str, str]) -> str:
+    """Find a ``@param`` description that matches a parsed input name.
+
+    Input names may be composite (e.g. ``val(meta), path(bam)``) so we check
+    each component name against the ``param_docs`` keys.  For a tuple input
+    the descriptions of all matching components are joined.
+
+    Args:
+        input_name: The parsed input name (e.g. ``"val(meta), path(bam)"`` or ``"reads"``).
+        param_docs: Dict mapping param names to their Groovydoc descriptions.
+
+    Returns:
+        The matching description, or an empty string if none found.
+    """
+    if not param_docs:
+        return ""
+
+    # Direct match (simple inputs like "reads")
+    if input_name in param_docs:
+        return param_docs[input_name]
+
+    # For composite/tuple inputs, extract component names and look them up
+    # Matches val(meta), path(bam), file(reads), env(x), etc.
+    component_names = re.findall(r"(?:val|path|file|env)\((\w+)\)", input_name)
+    if not component_names:
+        return ""
+
+    descriptions = []
+    for comp_name in component_names:
+        if comp_name in param_docs:
+            descriptions.append(f"`{comp_name}`: {param_docs[comp_name]}")
+
+    return "; ".join(descriptions) if descriptions else ""
+
+
+def _parse_groovydoc_from_source(
+    source_path: Path,
+    process_name: str,
+) -> tuple[str, dict[str, str]]:
+    """Parse a Groovydoc comment from a ``.nf`` source file.
+
+    When the Nextflow LSP does not return a docstring (common with typed
+    processes), this function reads the source file and extracts the
+    ``/** ... */`` comment block preceding the process definition.
+
+    Supports two documentation styles:
+
+    1. Standard Groovydoc ``@param`` / ``@return`` tags::
+
+        /** @param meta  Sample metadata map
+         *  @return txt  Output text file
+         */
+
+    2. Bullet-list ``Inputs:`` / ``Outputs:`` sections::
+
+        /** Inputs:
+         *   - - meta: sample metadata map
+         *     - bam: input BAM file
+         *  Outputs:
+         *   - - txt: output text file
+         */
+
+    Args:
+        source_path: Absolute path to the ``.nf`` source file.
+        process_name: Name of the process to locate.
+
+    Returns:
+        Tuple of ``(docstring, param_docs)`` where *docstring* is the free-text
+        description and *param_docs* maps param/return names to descriptions.
+        Returns ``("", {})`` if no Groovydoc is found.
+    """
+    try:
+        source = source_path.read_text(encoding="utf-8")
+    except OSError as e:
+        logger.debug(f"Could not read source file {source_path} for Groovydoc: {e}")
+        return "", {}
+
+    # Find the process declaration, then look backwards for the nearest /** ... */
+    proc_pattern = re.compile(
+        r"process\s+" + re.escape(process_name) + r"\s*\{",
+    )
+    proc_match = proc_pattern.search(source)
+    if not proc_match:
+        return "", {}
+
+    # Search the text before the process for the last /** ... */ comment
+    preceding = source[: proc_match.start()]
+    # Find all /** ... */ blocks and take the last one (closest to the process)
+    comment_matches = list(re.finditer(r"/\*\*(.*?)\*/", preceding, re.DOTALL))
+    if not comment_matches:
+        return "", {}
+
+    comment_body = comment_matches[-1].group(1)
+    return _parse_groovydoc_comment(comment_body)
+
+
+def _parse_groovydoc_comment(comment_body: str) -> tuple[str, dict[str, str]]:
+    """Parse the body of a ``/** ... */`` Groovydoc comment.
+
+    Handles both ``@param``/``@return`` tags and ``Inputs:``/``Outputs:``
+    bullet-list sections.
+
+    Args:
+        comment_body: The text between ``/**`` and ``*/``.
+
+    Returns:
+        Tuple of ``(docstring, param_docs)``.
+    """
+    lines = comment_body.split("\n")
+    doc_lines: list[str] = []
+    params: dict[str, str] = {}
+    current_section = "description"
+    current_param = ""
+
+    for raw_line in lines:
+        # Strip leading whitespace and * characters (Groovydoc format)
+        line = raw_line.strip()
+        if line.startswith("*"):
+            line = line[1:].strip()
+
+        if not line:
+            if current_section == "description" and doc_lines:
+                doc_lines.append("")  # preserve paragraph breaks
+            continue
+
+        # --- Standard @param / @return tags ---
+
+        # Check for @param tag
+        param_match = re.match(r"@param\s+(\w+)\s*(.*)", line)
+        if param_match:
+            current_section = "param"
+            current_param = param_match.group(1)
+            params[current_param] = param_match.group(2).strip()
+            continue
+
+        # Check for @return tag (named: @return name desc)
+        return_named = re.match(r"@returns?\s+(\w+)\s+(.*)", line)
+        if return_named:
+            current_section = "return"
+            current_param = f"_return_{return_named.group(1)}"
+            params[current_param] = return_named.group(2).strip()
+            continue
+
+        # Check for @return tag (unnamed: @return desc)
+        return_unnamed = re.match(r"@returns?\s*(.*)", line)
+        if return_unnamed:
+            current_section = "return"
+            current_param = "_return"
+            params["_return"] = return_unnamed.group(1).strip()
+            continue
+
+        # --- Bullet-list Inputs: / Outputs: sections ---
+
+        # Check for section headers
+        if re.match(r"Inputs?:", line, re.IGNORECASE):
+            current_section = "input_bullets"
+            continue
+        if re.match(r"Outputs?:", line, re.IGNORECASE):
+            current_section = "output_bullets"
+            continue
+
+        # Check for bullet items: "- name: description" or "- - name: description"
+        bullet_match = re.match(r"-\s*-?\s*(\w+)\s*:\s*(.*)", line)
+        if bullet_match and current_section in ("input_bullets", "output_bullets"):
+            name = bullet_match.group(1)
+            desc = bullet_match.group(2).strip()
+            if current_section == "input_bullets":
+                current_param = name
+                params[name] = desc
+            else:
+                current_param = f"_return_{name}"
+                params[current_param] = desc
+            continue
+
+        # Handle continuation lines
+        if current_section == "description":
+            # Skip the process name if it's the first line (e.g. "/** SV_PILEUP")
+            if not doc_lines and re.match(r"^[A-Z_0-9]+$", line):
+                continue
+            doc_lines.append(line)
+        elif current_section in ("param", "return", "input_bullets", "output_bullets"):
+            if current_param and line and not line.startswith("@"):
+                params[current_param] += " " + line
+
+    docstring = "\n".join(doc_lines).strip()
+    return docstring, params
diff --git a/src/nf_docs/lsp_client.py b/src/nf_docs/lsp_client.py
index 8f251dd..f6e0e74 100644
--- a/src/nf_docs/lsp_client.py
+++ b/src/nf_docs/lsp_client.py
@@ -872,18 +872,27 @@ def parse_hover_content(hover: dict[str, Any] | None) -> tuple[str, str, dict[st
                 params[current_param] = param_match.group(2).strip()
                 continue
 
-            # Check for @return tag
-            return_match = re.match(r"@returns?\s*(.*)", line_stripped)
+            # Check for @return tag (supports both named and unnamed forms)
+            # Named:   @return txt  Description of output
+            # Unnamed: @return Description of single return value
+            return_match = re.match(r"@returns?\s+(\w+)\s+(.*)", line_stripped)
             if return_match:
                 current_section = "return"
-                params["_return"] = return_match.group(1).strip()
+                current_param = f"_return_{return_match.group(1)}"
+                params[current_param] = return_match.group(2).strip()
+                continue
+            return_unnamed = re.match(r"@returns?\s*(.*)", line_stripped)
+            if return_unnamed:
+                current_section = "return"
+                current_param = "_return"
+                params["_return"] = return_unnamed.group(1).strip()
                 continue
 
             # Handle continuation lines
             if current_section == "description":
                 if line_stripped and not line_stripped.startswith("@"):
                     doc_lines.append(line_stripped)
-            elif current_section == "param" and current_param:
+            elif current_section in ("param", "return") and current_param:
                 if line_stripped and not line_stripped.startswith("@"):
                     params[current_param] += " " + line_stripped
 
diff --git a/src/nf_docs/templates/html.html b/src/nf_docs/templates/html.html
index 48f023b..c0f58b1 100644
--- a/src/nf_docs/templates/html.html
+++ b/src/nf_docs/templates/html.html
@@ -459,6 +459,10 @@
         background-color: rgba(239, 68, 68, 0.2); /* red with opacity */
         color: rgb(252 165 165); /* red-300 */
       }
+      html.dark .bg-yellow-100 {
+        background-color: rgba(234, 179, 8, 0.2); /* yellow with opacity */
+        color: rgb(253 224 71); /* yellow-300 */
+      }
       html.dark .bg-green-100 {
         background-color: rgba(34, 197, 94, 0.2); /* green with opacity */
         color: rgb(134 239 172); /* green-300 */
@@ -1472,6 +1476,12 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">Pipeline Inputs</h1>
               >
                 {{ inp.format }}
               </span>
+              {% endif %} {% if inp.pattern %}
+              <span
+                class="inline-block px-2 py-0.5 rounded-full text-xs font-medium bg-yellow-100 text-yellow-800"
+              >
+                Pattern: <code class="font-mono">{{ inp.pattern }}</code>
+              </span>
               {% endif %} {% if inp.required %}
               <span
                 class="inline-block px-2 py-0.5 rounded-full text-xs font-medium bg-red-100 text-red-600"
@@ -1506,13 +1516,6 @@ <h1 class="text-3xl font-bold mb-4 text-slate-800">Pipeline Inputs</h1>
               <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm">{{ val }}</code>
               {% if not loop.last %}, {% endif %} {% endfor %}
             </p>
-            {% endif %} {% if inp.pattern %}
-            <p class="mt-2">
-              <strong>Pattern:</strong>
-              <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
-                >{{ inp.pattern }}</code
-              >
-            </p>
             {% endif %}
           </div>
           {% endfor %} {% endfor %}
@@ -1670,7 +1673,11 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Inputs (take)</h3>
                         >{{ inp.name|wbr }}</code
                       >
                     </td>
-                    <td class="p-3 border-b border-slate-200">{{ inp.description or '-' }}</td>
+                    <td class="p-3 border-b border-slate-200">
+                      {% if inp.description %}
+                      <div class="prose prose-sm">{{ inp.description|markdown }}</div>
+                      {% else %}-{% endif %}
+                    </td>
                   </tr>
                   {% endfor %} {% endif %}
                 </tbody>
@@ -1715,7 +1722,11 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs (emit)</h3>
                         >{{ out.name|wbr }}</code
                       >
                     </td>
-                    <td class="p-3 border-b border-slate-200">{{ out.description or '-' }}</td>
+                    <td class="p-3 border-b border-slate-200">
+                      {% if out.description %}
+                      <div class="prose prose-sm">{{ out.description|markdown }}</div>
+                      {% else %}-{% endif %}
+                    </td>
                   </tr>
                   {% endfor %} {% endif %}
                 </tbody>
@@ -1971,7 +1982,11 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Inputs</h3>
                         >{{ inp.type|wbr }}</code
                       >
                     </td>
-                    <td class="p-3 border-b border-slate-200">{{ inp.description or '-' }}</td>
+                    <td class="p-3 border-b border-slate-200">
+                      {% if inp.description %}
+                      <div class="prose prose-sm">{{ inp.description|markdown }}</div>
+                      {% else %}-{% endif %}
+                    </td>
                   </tr>
                   {% endfor %} {% endif %}
                 </tbody>
@@ -2047,7 +2062,11 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
                       >
                       {% else %}-{% endif %}
                     </td>
-                    <td class="p-3 border-b border-slate-200">{{ out.description or '-' }}</td>
+                    <td class="p-3 border-b border-slate-200">
+                      {% if out.description %}
+                      <div class="prose prose-sm">{{ out.description|markdown }}</div>
+                      {% else %}-{% endif %}
+                    </td>
                   </tr>
                   {% endfor %} {% endif %}
                 </tbody>
@@ -2189,7 +2208,11 @@ <h3 class="text-lg font-semibold mt-4 mb-2">Parameters</h3>
                         >{{ p.name|wbr }}</code
                       >
                     </td>
-                    <td class="p-3 border-b border-slate-200">{{ p.description or '-' }}</td>
+                    <td class="p-3 border-b border-slate-200">
+                      {% if p.description %}
+                      <div class="prose prose-sm">{{ p.description|markdown }}</div>
+                      {% else %}-{% endif %}
+                    </td>
                     <td class="p-3 border-b border-slate-200">
                       {% if p.default is not none %}
                       <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
diff --git a/src/nf_docs/templates/tailwind.css b/src/nf_docs/templates/tailwind.css
index 1bebbe8..d5c6900 100644
--- a/src/nf_docs/templates/tailwind.css
+++ b/src/nf_docs/templates/tailwind.css
@@ -1,2 +1,2 @@
 /*! tailwindcss v4.1.18 | MIT License | https://tailwindcss.com */
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diff --git a/tests/test_extractor.py b/tests/test_extractor.py
index 3339e66..321d31c 100644
--- a/tests/test_extractor.py
+++ b/tests/test_extractor.py
@@ -160,3 +160,125 @@ def test_parse_empty_name(self, tmp_path: Path):
         symbol_type, name = extractor._parse_symbol_name("")
         assert symbol_type == "unknown"
         assert name == ""
+
+
+class TestGroovydocParsing:
+    """Tests for Groovydoc parsing from source files."""
+
+    def test_parse_groovydoc_at_param_return(self):
+        """Parse standard @param and @return tags."""
+        from nf_docs.extractor import _parse_groovydoc_comment
+
+        comment = """
+         * Align reads to reference genome.
+         *
+         * @param meta  Map containing sample information
+         * @param bam   Input BAM file
+         * @return txt  Tuple of meta and output text file
+         * @return bam  Tuple of meta and output BAM file
+        """
+        docstring, params = _parse_groovydoc_comment(comment)
+        assert docstring == "Align reads to reference genome."
+        assert params["meta"] == "Map containing sample information"
+        assert params["bam"] == "Input BAM file"
+        assert params["_return_txt"] == "Tuple of meta and output text file"
+        assert params["_return_bam"] == "Tuple of meta and output BAM file"
+
+    def test_parse_groovydoc_bullet_format(self):
+        """Parse Inputs:/Outputs: bullet-list format."""
+        from nf_docs.extractor import _parse_groovydoc_comment
+
+        comment = """
+         * Detect structural variants.
+         *
+         * Inputs:
+         *   - - meta: Map of sample info
+         *     - bam: Input BAM file
+         * Outputs:
+         *   - - meta: Map of sample info
+         *     - txt: SvPileup breakpoint output
+        """
+        docstring, params = _parse_groovydoc_comment(comment)
+        assert docstring == "Detect structural variants."
+        assert params["meta"] == "Map of sample info"
+        assert params["bam"] == "Input BAM file"
+        assert params["_return_txt"] == "SvPileup breakpoint output"
+
+    def test_parse_groovydoc_from_source_with_intervening_code(self, tmp_path: Path):
+        """Groovydoc with code between */ and process declaration."""
+        from nf_docs.extractor import _parse_groovydoc_from_source
+
+        source = """\
+/**
+ * Detect SVs from BAM.
+ *
+ * @param meta  Sample metadata
+ * @param bam   Input BAM
+ * @return txt  Output text file
+ */
+nextflow.preview.types = true
+process SV_PILEUP {
+    input:
+    (meta, bam): Tuple<?, Path>
+
+    output:
+    txt
+    bam
+}
+"""
+        nf_file = tmp_path / "sv_pileup.nf"
+        nf_file.write_text(source)
+
+        docstring, params = _parse_groovydoc_from_source(nf_file, "SV_PILEUP")
+        assert "Detect SVs from BAM" in docstring
+        assert params["meta"] == "Sample metadata"
+        assert params["bam"] == "Input BAM"
+        assert params["_return_txt"] == "Output text file"
+
+    def test_parse_groovydoc_from_source_not_found(self, tmp_path: Path):
+        """Returns empty when process not found in source."""
+        from nf_docs.extractor import _parse_groovydoc_from_source
+
+        nf_file = tmp_path / "other.nf"
+        nf_file.write_text("process OTHER { script: '' }\n")
+
+        docstring, params = _parse_groovydoc_from_source(nf_file, "MISSING")
+        assert docstring == ""
+        assert params == {}
+
+    def test_parse_groovydoc_from_source_no_file(self, tmp_path: Path):
+        """Returns empty when source file doesn't exist."""
+        from nf_docs.extractor import _parse_groovydoc_from_source
+
+        docstring, params = _parse_groovydoc_from_source(tmp_path / "nonexistent.nf", "PROC")
+        assert docstring == ""
+        assert params == {}
+
+    def test_find_param_description_simple(self):
+        """Match a simple input name to param docs."""
+        from nf_docs.extractor import _find_param_description
+
+        param_docs = {"reads": "FASTQ input files", "genome": "Reference genome"}
+        assert _find_param_description("reads", param_docs) == "FASTQ input files"
+
+    def test_find_param_description_tuple(self):
+        """Match tuple component names to param docs."""
+        from nf_docs.extractor import _find_param_description
+
+        param_docs = {
+            "meta": "Sample metadata map",
+            "bam": "Input BAM file",
+        }
+        desc = _find_param_description("val(meta), path(bam)", param_docs)
+        assert "meta" in desc
+        assert "Sample metadata map" in desc
+        assert "bam" in desc
+        assert "Input BAM file" in desc
+
+    def test_find_param_description_no_match(self):
+        """Returns empty when no param docs match."""
+        from nf_docs.extractor import _find_param_description
+
+        assert _find_param_description("unknown", {"meta": "desc"}) == ""
+        assert _find_param_description("val(x)", {"meta": "desc"}) == ""
+        assert _find_param_description("reads", {}) == ""

From 472ad33b44ab7d426485aa91fc857f67f579130b Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Tue, 3 Mar 2026 20:14:56 +0100
Subject: [PATCH 7/9] Add nf-fgsv as example pipeline

Fulcrum Genomics structural variant calling pipeline, demonstrating
typed Nextflow syntax (nextflow.preview.types) with Groovydoc support.
---
 docs/examples.md                             |    1 +
 docs/examples/nf-fgsv/index.html             | 3218 ++++++++++++++++++
 docs/examples/nf-fgsv/json/pipeline-api.json |  153 +
 docs/examples/nf-fgsv/markdown/index.md      |   30 +
 docs/examples/nf-fgsv/markdown/inputs.md     |   20 +
 docs/examples/nf-fgsv/markdown/processes.md  |   94 +
 docs/examples/nf-fgsv/markdown/workflows.md  |   19 +
 7 files changed, 3535 insertions(+)
 create mode 100644 docs/examples/nf-fgsv/index.html
 create mode 100644 docs/examples/nf-fgsv/json/pipeline-api.json
 create mode 100644 docs/examples/nf-fgsv/markdown/index.md
 create mode 100644 docs/examples/nf-fgsv/markdown/inputs.md
 create mode 100644 docs/examples/nf-fgsv/markdown/processes.md
 create mode 100644 docs/examples/nf-fgsv/markdown/workflows.md

diff --git a/docs/examples.md b/docs/examples.md
index e57c05f..507b899 100644
--- a/docs/examples.md
+++ b/docs/examples.md
@@ -8,4 +8,5 @@ Generated documentation for real-world Nextflow pipelines.
 | rnaseq-nf       | Simple RNA-seq pipeline                      | [HTML](examples/rnaseq-nf/index.html)       | [Markdown](examples/rnaseq-nf/markdown/index.md)       | [JSON](examples/rnaseq-nf/json/pipeline-api.json)       |
 | rnavar          | nf-core/rnavar — RNA variant calling         | [HTML](examples/rnavar/index.html)          | [Markdown](examples/rnavar/markdown/index.md)          | [JSON](examples/rnavar/json/pipeline-api.json)          |
 | sarek           | nf-core/sarek — variant calling & annotation | [HTML](examples/sarek/index.html)           | [Markdown](examples/sarek/markdown/index.md)           | [JSON](examples/sarek/json/pipeline-api.json)           |
+| nf-fgsv         | Fulcrum Genomics structural variant calling  | [HTML](examples/nf-fgsv/index.html)         | [Markdown](examples/nf-fgsv/markdown/index.md)         | [JSON](examples/nf-fgsv/json/pipeline-api.json)         |
 | wf-metagenomics | Oxford Nanopore metagenomics workflow        | [HTML](examples/wf-metagenomics/index.html) | [Markdown](examples/wf-metagenomics/markdown/index.md) | [JSON](examples/wf-metagenomics/json/pipeline-api.json) |
diff --git a/docs/examples/nf-fgsv/index.html b/docs/examples/nf-fgsv/index.html
new file mode 100644
index 0000000..0b8b4e3
--- /dev/null
+++ b/docs/examples/nf-fgsv/index.html
@@ -0,0 +1,3218 @@
+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>nf-fgsv workflow parameters</title>
+    <script>
+      // Apply theme before page renders to avoid flash
+      (function () {
+        const STORAGE_KEY = "nf-docs-theme";
+        const stored = localStorage.getItem(STORAGE_KEY);
+        let theme = stored;
+        if (!theme) {
+          // Auto-detect from OS preference
+          theme = window.matchMedia("(prefers-color-scheme: dark)").matches ? "dark" : "light";
+        }
+        if (theme === "dark") {
+          document.documentElement.classList.add("dark");
+        }
+      })();
+    </script>
+    <style>
+      /* Tailwind CSS will be injected here */
+
+      /* Prose styles for rendered markdown content */
+      .prose p {
+        margin-bottom: 1em;
+      }
+      .prose p:last-child {
+        margin-bottom: 0;
+      }
+      .prose ul,
+      .prose ol {
+        margin-top: 0.5em;
+        margin-bottom: 1em;
+        padding-left: 1.5em;
+      }
+      .prose ul {
+        list-style-type: disc;
+      }
+      .prose ol {
+        list-style-type: decimal;
+      }
+      .prose li {
+        margin-bottom: 0.25em;
+      }
+      .prose li:last-child {
+        margin-bottom: 0;
+      }
+      .prose code {
+        background-color: rgb(241 245 249); /* slate-100 */
+        padding: 0.125rem 0.375rem;
+        border-radius: 0.25rem;
+        font-family: ui-monospace, monospace;
+        font-size: 0.875em;
+      }
+      .prose pre {
+        background-color: rgb(30 41 59); /* slate-800 */
+        color: rgb(226 232 240); /* slate-200 */
+        padding: 1rem;
+        border-radius: 0.5rem;
+        overflow-x: auto;
+        margin: 1em 0;
+      }
+      .prose pre code {
+        background: none;
+        padding: 0;
+        color: inherit;
+      }
+      .prose a {
+        color: #0dc09d;
+        text-decoration: underline;
+      }
+      .prose a:hover {
+        color: #0a9a7d;
+      }
+      .prose a.paragraph-link {
+        text-decoration: none;
+        color: rgb(148 163 184); /* slate-400 - match non-prose paragraph-link */
+        opacity: 0.7;
+      }
+      .prose .heading-anchor:hover a.paragraph-link {
+        opacity: 1;
+        color: #0dc09d; /* primary */
+      }
+      .prose blockquote {
+        border-left: 4px solid rgb(203 213 225); /* slate-300 */
+        padding-left: 1em;
+        margin: 1em 0;
+        color: rgb(100 116 139); /* slate-500 */
+        font-style: italic;
+      }
+      .prose h1,
+      .prose h2,
+      .prose h3,
+      .prose h4,
+      .prose h5,
+      .prose h6 {
+        font-weight: 600;
+        margin-top: 1.5em;
+        margin-bottom: 0.5em;
+      }
+      .prose h1 {
+        font-size: 1.5em;
+      }
+      .prose h2 {
+        font-size: 1.25em;
+      }
+      .prose h3 {
+        font-size: 1.125em;
+      }
+      .prose table {
+        width: 100%;
+        border-collapse: collapse;
+        margin: 1em 0;
+      }
+      .prose th,
+      .prose td {
+        border: 1px solid rgb(226 232 240); /* slate-200 */
+        padding: 0.5rem;
+        text-align: left;
+      }
+      .prose th {
+        background-color: rgb(241 245 249); /* slate-100 */
+        font-weight: 600;
+      }
+      /* Search results highlighting */
+      .search-highlight {
+        background-color: rgb(254 249 195); /* yellow-100 */
+        padding: 0.125rem 0.25rem;
+        border-radius: 0.25rem;
+      }
+      /* Scroll offset for fixed top nav */
+      [id] {
+        scroll-margin-top: 4.5rem; /* 3.5rem nav + 1rem padding */
+      }
+
+      /* Prevent horizontal overflow on main content */
+      main {
+        overflow-x: hidden;
+      }
+
+      /* Paragraph anchor links */
+      .paragraph-link {
+        margin-left: 0.5rem;
+        color: rgb(148 163 184); /* slate-400 */
+        opacity: 0.7;
+        transition:
+          opacity 0.2s,
+          color 0.2s;
+        text-decoration: none;
+      }
+      .heading-anchor:hover .paragraph-link {
+        opacity: 1;
+        color: #0dc09d; /* primary */
+      }
+
+      /* Dark mode paragraph links */
+      html.dark .paragraph-link {
+        color: rgb(100 116 139); /* slate-500 */
+        opacity: 0.8;
+      }
+      html.dark .heading-anchor:hover .paragraph-link {
+        opacity: 1;
+        color: #0dc09d; /* primary */
+      }
+
+      /* ==================== Dark Mode Styles ==================== */
+
+      /* Theme toggle button */
+      .theme-toggle {
+        display: flex;
+        align-items: center;
+        justify-content: center;
+        width: 2rem;
+        height: 2rem;
+        border-radius: 0.375rem;
+        cursor: pointer;
+        transition: background-color 0.2s;
+      }
+      .theme-toggle:hover {
+        background-color: rgb(241 245 249); /* slate-100 */
+      }
+      .theme-toggle svg {
+        width: 1.25rem;
+        height: 1.25rem;
+        color: rgb(100 116 139); /* slate-500 */
+      }
+      .theme-toggle:hover svg {
+        color: rgb(71 85 105); /* slate-600 */
+      }
+      /* Hide icons based on current theme */
+      .theme-toggle .icon-sun {
+        display: none;
+      }
+      .theme-toggle .icon-moon {
+        display: block;
+      }
+
+      /* Dark mode base styles */
+      html.dark body {
+        background-color: rgb(15 23 42); /* slate-900 */
+        color: rgb(226 232 240); /* slate-200 */
+      }
+      html.dark .theme-toggle:hover {
+        background-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark .theme-toggle svg {
+        color: rgb(148 163 184); /* slate-400 */
+      }
+      html.dark .theme-toggle:hover svg {
+        color: rgb(226 232 240); /* slate-200 */
+      }
+      html.dark .theme-toggle .icon-sun {
+        display: block;
+      }
+      html.dark .theme-toggle .icon-moon {
+        display: none;
+      }
+
+      /* Dark mode - Header */
+      html.dark header {
+        background-color: rgb(30 41 59); /* slate-800 */
+        border-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark header .text-slate-500 {
+        color: rgb(148 163 184); /* slate-400 */
+      }
+      html.dark header .text-slate-600 {
+        color: rgb(148 163 184); /* slate-400 */
+      }
+
+      /* Dark mode - Search input */
+      html.dark #search-input {
+        background-color: rgb(51 65 85); /* slate-700 */
+        border-color: rgb(71 85 105); /* slate-600 */
+        color: rgb(226 232 240); /* slate-200 */
+      }
+      html.dark #search-input::placeholder {
+        color: rgb(148 163 184); /* slate-400 */
+      }
+      html.dark #search-input:focus {
+        border-color: transparent;
+      }
+      html.dark #search-clear {
+        color: rgb(148 163 184); /* slate-400 */
+      }
+      html.dark #search-clear:hover {
+        color: rgb(226 232 240); /* slate-200 */
+      }
+
+      /* Dark mode - Left sidebar */
+      html.dark #left-nav {
+        background-color: rgb(30 41 59); /* slate-800 */
+        border-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark .nav-link {
+        color: rgb(203 213 225); /* slate-300 */
+      }
+      html.dark .nav-link:hover:not(.bg-primary) {
+        background-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark .nav-link.text-slate-800 {
+        color: rgb(203 213 225); /* slate-300 */
+      }
+      /* Active nav link in dark mode - ensure bright white text */
+      html.dark .nav-link.bg-primary {
+        color: rgb(255 255 255); /* white */
+      }
+
+      /* Light mode - don't apply hover to active nav link */
+      .nav-link.bg-primary:hover {
+        background-color: #0dc09d; /* keep primary background on hover */
+      }
+
+      /* Dark mode - Mobile menu */
+      html.dark #mobile-menu {
+        background-color: rgb(30 41 59); /* slate-800 */
+      }
+      html.dark #mobile-menu .border-slate-200 {
+        border-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark .mobile-nav-link {
+        color: rgb(203 213 225); /* slate-300 */
+      }
+      html.dark .mobile-nav-link:hover {
+        background-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark #mobile-toc-link {
+        color: rgb(203 213 225); /* slate-300 */
+      }
+      html.dark #mobile-toc-link:hover {
+        background-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark #mobile-toc-back {
+        color: rgb(203 213 225); /* slate-300 */
+      }
+      html.dark #mobile-toc-back:hover {
+        background-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark #mobile-toc-nav .sticky {
+        background-color: rgb(30 41 59); /* slate-800 */
+        border-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark .mobile-toc-link {
+        color: rgb(148 163 184); /* slate-400 */
+      }
+      html.dark .mobile-toc-link:hover {
+        background-color: rgb(51 65 85); /* slate-700 */
+        color: rgb(226 232 240); /* slate-200 */
+      }
+      html.dark .mobile-toc-group-header {
+        color: rgb(203 213 225); /* slate-300 */
+      }
+      html.dark #mobile-search-input {
+        background-color: rgb(51 65 85); /* slate-700 */
+        border-color: rgb(71 85 105); /* slate-600 */
+        color: rgb(226 232 240); /* slate-200 */
+      }
+      html.dark #mobile-search-input::placeholder {
+        color: rgb(148 163 184); /* slate-400 */
+      }
+
+      /* Dark mode - Right sidebar */
+      html.dark #right-nav {
+        background-color: rgb(30 41 59); /* slate-800 */
+        border-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark #right-nav .text-slate-500 {
+        color: rgb(148 163 184); /* slate-400 */
+      }
+      html.dark .toc-group-header {
+        color: rgb(203 213 225); /* slate-300 */
+      }
+      html.dark .toc-link {
+        color: rgb(148 163 184); /* slate-400 */
+      }
+      html.dark .toc-link:hover {
+        background-color: rgb(51 65 85); /* slate-700 */
+        color: rgb(226 232 240); /* slate-200 */
+      }
+
+      /* Dark mode - Main content */
+      html.dark main {
+        background-color: rgb(15 23 42); /* slate-900 */
+      }
+      html.dark .text-slate-800 {
+        color: rgb(226 232 240); /* slate-200 */
+      }
+      html.dark .text-slate-600 {
+        color: rgb(148 163 184); /* slate-400 */
+      }
+      html.dark .text-slate-500 {
+        color: rgb(148 163 184); /* slate-400 */
+      }
+      html.dark .text-slate-400 {
+        color: rgb(100 116 139); /* slate-500 */
+      }
+      html.dark .text-slate-300 {
+        color: rgb(71 85 105); /* slate-600 */
+      }
+      html.dark .border-slate-200 {
+        border-color: rgb(51 65 85); /* slate-700 */
+      }
+
+      /* Dark mode - Cards and panels */
+      html.dark .bg-white {
+        background-color: rgb(30 41 59); /* slate-800 */
+      }
+      html.dark .bg-slate-50 {
+        background-color: rgb(15 23 42); /* slate-900 */
+      }
+      html.dark .bg-slate-100 {
+        background-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark .hover\:bg-slate-50:hover {
+        background-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark .hover\:bg-slate-100:hover {
+        background-color: rgb(51 65 85); /* slate-700 */
+      }
+
+      /* Dark mode - Keyword badges */
+      html.dark .bg-slate-200 {
+        background-color: rgb(51 65 85); /* slate-700 */
+        color: rgb(203 213 225); /* slate-300 */
+      }
+
+      /* nf-core module link */
+      .nfcore-link {
+        opacity: 0.3;
+        transition: opacity 0.2s;
+        vertical-align: middle;
+      }
+      .nfcore-link:hover,
+      .heading-anchor:hover .nfcore-link {
+        opacity: 1;
+      }
+      .nfcore-link svg {
+        width: 1em;
+        height: 1em;
+        display: inline-block;
+        vertical-align: -0.125em;
+      }
+
+      /* Dark mode - Tables */
+      html.dark th {
+        background-color: rgb(51 65 85); /* slate-700 */
+        color: rgb(226 232 240); /* slate-200 */
+      }
+      html.dark td {
+        border-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark tr:hover {
+        background-color: rgb(51 65 85); /* slate-700 */
+      }
+
+      /* Dark mode - Code blocks */
+      html.dark .prose code {
+        background-color: rgb(51 65 85); /* slate-700 */
+        color: rgb(226 232 240); /* slate-200 */
+      }
+      html.dark code.bg-slate-100 {
+        background-color: rgb(51 65 85); /* slate-700 */
+        color: rgb(226 232 240); /* slate-200 */
+      }
+
+      /* Dark mode - Prose blockquote */
+      html.dark .prose blockquote {
+        border-color: rgb(71 85 105); /* slate-600 */
+        color: rgb(148 163 184); /* slate-400 */
+      }
+
+      /* Dark mode - Prose table */
+      html.dark .prose th,
+      html.dark .prose td {
+        border-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark .prose th {
+        background-color: rgb(51 65 85); /* slate-700 */
+      }
+
+      /* Dark mode - Prose paragraph links */
+      html.dark .prose a.paragraph-link {
+        color: rgb(100 116 139); /* slate-500 */
+        opacity: 0.8;
+      }
+      html.dark .prose .heading-anchor:hover a.paragraph-link {
+        opacity: 1;
+        color: #0dc09d; /* primary */
+      }
+
+      /* Dark mode - Badges/tags */
+      html.dark .bg-purple-100 {
+        background-color: rgba(139, 92, 246, 0.2); /* purple with opacity */
+        color: rgb(196 181 253); /* purple-300 */
+      }
+      html.dark .bg-red-100 {
+        background-color: rgba(239, 68, 68, 0.2); /* red with opacity */
+        color: rgb(252 165 165); /* red-300 */
+      }
+      html.dark .bg-yellow-100 {
+        background-color: rgba(234, 179, 8, 0.2); /* yellow with opacity */
+        color: rgb(253 224 71); /* yellow-300 */
+      }
+      html.dark .bg-green-100 {
+        background-color: rgba(34, 197, 94, 0.2); /* green with opacity */
+        color: rgb(134 239 172); /* green-300 */
+      }
+      html.dark .bg-primary-light {
+        background-color: rgba(13, 192, 157, 0.2); /* primary with opacity */
+      }
+
+      /* Dark mode - Search highlight */
+      html.dark .search-highlight {
+        background-color: rgba(234, 179, 8, 0.3); /* yellow with opacity */
+        color: rgb(253 224 71); /* yellow-300 */
+      }
+
+      /* Dark mode - Help text background */
+      html.dark .prose.bg-slate-100 {
+        background-color: rgb(51 65 85); /* slate-700 */
+      }
+
+      /* ==================== GitHub-style Alerts ==================== */
+
+      .alert {
+        padding: 1rem;
+        margin: 1em 0;
+        border-radius: 0.375rem;
+        border-left-width: 4px;
+        border-left-style: solid;
+      }
+      .alert-title {
+        display: flex;
+        align-items: center;
+        gap: 0.5rem;
+        font-weight: 600;
+        margin-bottom: 0.5rem;
+      }
+      .alert-icon {
+        flex-shrink: 0;
+        fill: currentColor;
+      }
+      .alert-content {
+        margin: 0;
+      }
+      .alert-content p:first-child {
+        margin-top: 0;
+      }
+      .alert-content p:last-child {
+        margin-bottom: 0;
+      }
+
+      /* Note - Blue */
+      .alert-note {
+        background-color: rgb(239 246 255); /* blue-50 */
+        border-left-color: rgb(59 130 246); /* blue-500 */
+      }
+      .alert-note .alert-title {
+        color: rgb(29 78 216); /* blue-700 */
+      }
+
+      /* Tip - Green */
+      .alert-tip {
+        background-color: rgb(240 253 244); /* green-50 */
+        border-left-color: rgb(34 197 94); /* green-500 */
+      }
+      .alert-tip .alert-title {
+        color: rgb(21 128 61); /* green-700 */
+      }
+
+      /* Important - Purple */
+      .alert-important {
+        background-color: rgb(250 245 255); /* purple-50 */
+        border-left-color: rgb(168 85 247); /* purple-500 */
+      }
+      .alert-important .alert-title {
+        color: rgb(126 34 206); /* purple-700 */
+      }
+
+      /* Warning - Yellow/Amber */
+      .alert-warning {
+        background-color: rgb(254 252 232); /* yellow-50 */
+        border-left-color: rgb(234 179 8); /* yellow-500 */
+      }
+      .alert-warning .alert-title {
+        color: rgb(161 98 7); /* yellow-700 */
+      }
+
+      /* Caution - Red */
+      .alert-caution {
+        background-color: rgb(254 242 242); /* red-50 */
+        border-left-color: rgb(239 68 68); /* red-500 */
+      }
+      .alert-caution .alert-title {
+        color: rgb(185 28 28); /* red-700 */
+      }
+
+      /* ==================== Dark Mode Alerts ==================== */
+
+      html.dark .alert-note {
+        background-color: rgba(59, 130, 246, 0.1); /* blue with opacity */
+        border-left-color: rgb(96 165 250); /* blue-400 */
+      }
+      html.dark .alert-note .alert-title {
+        color: rgb(147 197 253); /* blue-300 */
+      }
+
+      html.dark .alert-tip {
+        background-color: rgba(34, 197, 94, 0.1); /* green with opacity */
+        border-left-color: rgb(74 222 128); /* green-400 */
+      }
+      html.dark .alert-tip .alert-title {
+        color: rgb(134 239 172); /* green-300 */
+      }
+
+      html.dark .alert-important {
+        background-color: rgba(168, 85, 247, 0.1); /* purple with opacity */
+        border-left-color: rgb(192 132 252); /* purple-400 */
+      }
+      html.dark .alert-important .alert-title {
+        color: rgb(216 180 254); /* purple-300 */
+      }
+
+      html.dark .alert-warning {
+        background-color: rgba(234, 179, 8, 0.1); /* yellow with opacity */
+        border-left-color: rgb(250 204 21); /* yellow-400 */
+      }
+      html.dark .alert-warning .alert-title {
+        color: rgb(253 224 71); /* yellow-300 */
+      }
+
+      html.dark .alert-caution {
+        background-color: rgba(239, 68, 68, 0.1); /* red with opacity */
+        border-left-color: rgb(248 113 113); /* red-400 */
+      }
+      html.dark .alert-caution .alert-title {
+        color: rgb(252 165 165); /* red-300 */
+      }
+
+      /* ==================== Syntax Highlighting (Pygments) ==================== */
+
+      /* Code block container styling - dark background in both light and dark modes */
+      .highlight {
+        background: rgb(30 41 59); /* slate-800 */
+        color: #c9d1d9; /* light gray text */
+        border-radius: 0.5rem;
+        padding: 1rem;
+        overflow-x: auto;
+        margin: 1em 0;
+      }
+      .highlight pre {
+        margin: 0;
+        background: none;
+        padding: 0;
+        line-height: 1.5;
+        color: inherit;
+      }
+      /* Override .prose code styles inside .highlight with high specificity */
+      .prose .highlight code,
+      .highlight code {
+        background: none !important;
+        padding: 0 !important;
+        font-size: 0.875em;
+        color: inherit;
+      }
+
+      /* Syntax highlighting - dark theme for both light and dark modes */
+      .highlight .hll {
+        background-color: #49483e;
+      }
+      .highlight .c {
+        color: #8b949e;
+      } /* Comment */
+      .highlight .err {
+        color: #f97583;
+      } /* Error */
+      .highlight .k {
+        color: #ff7b72;
+      } /* Keyword */
+      .highlight .o {
+        color: #ff7b72;
+      } /* Operator */
+      .highlight .ch {
+        color: #8b949e;
+      } /* Comment.Hashbang */
+      .highlight .cm {
+        color: #8b949e;
+      } /* Comment.Multiline */
+      .highlight .cp {
+        color: #ff7b72;
+      } /* Comment.Preproc */
+      .highlight .cpf {
+        color: #8b949e;
+      } /* Comment.PreprocFile */
+      .highlight .c1 {
+        color: #8b949e;
+      } /* Comment.Single */
+      .highlight .cs {
+        color: #8b949e;
+      } /* Comment.Special */
+      .highlight .gd {
+        color: #ffa198;
+        background-color: #490202;
+      } /* Generic.Deleted */
+      .highlight .ge {
+        font-style: italic;
+      } /* Generic.Emph */
+      .highlight .gr {
+        color: #ffa198;
+      } /* Generic.Error */
+      .highlight .gh {
+        color: #79c0ff;
+        font-weight: 600;
+      } /* Generic.Heading */
+      .highlight .gi {
+        color: #56d364;
+        background-color: #0f5323;
+      } /* Generic.Inserted */
+      .highlight .go {
+        color: #8b949e;
+      } /* Generic.Output */
+      .highlight .gp {
+        color: #8b949e;
+        font-weight: 600;
+      } /* Generic.Prompt */
+      .highlight .gs {
+        font-weight: 600;
+      } /* Generic.Strong */
+      .highlight .gu {
+        color: #d2a8ff;
+        font-weight: 600;
+      } /* Generic.Subheading */
+      .highlight .gt {
+        color: #ffa198;
+      } /* Generic.Traceback */
+      .highlight .kc {
+        color: #79c0ff;
+      } /* Keyword.Constant */
+      .highlight .kd {
+        color: #ff7b72;
+      } /* Keyword.Declaration */
+      .highlight .kn {
+        color: #ff7b72;
+      } /* Keyword.Namespace */
+      .highlight .kp {
+        color: #ff7b72;
+      } /* Keyword.Pseudo */
+      .highlight .kr {
+        color: #ff7b72;
+      } /* Keyword.Reserved */
+      .highlight .kt {
+        color: #d2a8ff;
+      } /* Keyword.Type */
+      .highlight .m {
+        color: #79c0ff;
+      } /* Literal.Number */
+      .highlight .s {
+        color: #a5d6ff;
+      } /* Literal.String */
+      .highlight .na {
+        color: #d2a8ff;
+      } /* Name.Attribute */
+      .highlight .nb {
+        color: #79c0ff;
+      } /* Name.Builtin */
+      .highlight .nc {
+        color: #f0883e;
+        font-weight: 600;
+      } /* Name.Class */
+      .highlight .no {
+        color: #79c0ff;
+      } /* Name.Constant */
+      .highlight .nd {
+        color: #d2a8ff;
+      } /* Name.Decorator */
+      .highlight .ni {
+        color: #c9d1d9;
+      } /* Name.Entity */
+      .highlight .ne {
+        color: #f0883e;
+        font-weight: 600;
+      } /* Name.Exception */
+      .highlight .nf {
+        color: #d2a8ff;
+      } /* Name.Function */
+      .highlight .nl {
+        color: #79c0ff;
+      } /* Name.Label */
+      .highlight .nn {
+        color: #ff7b72;
+      } /* Name.Namespace */
+      .highlight .nt {
+        color: #7ee787;
+      } /* Name.Tag */
+      .highlight .nv {
+        color: #ffa657;
+      } /* Name.Variable */
+      .highlight .ow {
+        color: #ff7b72;
+        font-weight: 600;
+      } /* Operator.Word */
+      .highlight .w {
+        color: #6e7681;
+      } /* Text.Whitespace */
+      .highlight .mb {
+        color: #79c0ff;
+      } /* Literal.Number.Bin */
+      .highlight .mf {
+        color: #79c0ff;
+      } /* Literal.Number.Float */
+      .highlight .mh {
+        color: #79c0ff;
+      } /* Literal.Number.Hex */
+      .highlight .mi {
+        color: #79c0ff;
+      } /* Literal.Number.Integer */
+      .highlight .mo {
+        color: #79c0ff;
+      } /* Literal.Number.Oct */
+      .highlight .sa {
+        color: #a5d6ff;
+      } /* Literal.String.Affix */
+      .highlight .sb {
+        color: #a5d6ff;
+      } /* Literal.String.Backtick */
+      .highlight .sc {
+        color: #a5d6ff;
+      } /* Literal.String.Char */
+      .highlight .dl {
+        color: #a5d6ff;
+      } /* Literal.String.Delimiter */
+      .highlight .sd {
+        color: #a5d6ff;
+      } /* Literal.String.Doc */
+      .highlight .s2 {
+        color: #a5d6ff;
+      } /* Literal.String.Double */
+      .highlight .se {
+        color: #79c0ff;
+      } /* Literal.String.Escape */
+      .highlight .sh {
+        color: #a5d6ff;
+      } /* Literal.String.Heredoc */
+      .highlight .si {
+        color: #a5d6ff;
+      } /* Literal.String.Interpol */
+      .highlight .sx {
+        color: #a5d6ff;
+      } /* Literal.String.Other */
+      .highlight .sr {
+        color: #a5d6ff;
+      } /* Literal.String.Regex */
+      .highlight .s1 {
+        color: #a5d6ff;
+      } /* Literal.String.Single */
+      .highlight .ss {
+        color: #79c0ff;
+      } /* Literal.String.Symbol */
+      .highlight .bp {
+        color: #79c0ff;
+      } /* Name.Builtin.Pseudo */
+      .highlight .fm {
+        color: #d2a8ff;
+      } /* Name.Function.Magic */
+      .highlight .vc {
+        color: #ffa657;
+      } /* Name.Variable.Class */
+      .highlight .vg {
+        color: #ffa657;
+      } /* Name.Variable.Global */
+      .highlight .vi {
+        color: #ffa657;
+      } /* Name.Variable.Instance */
+      .highlight .vm {
+        color: #ffa657;
+      } /* Name.Variable.Magic */
+      .highlight .il {
+        color: #79c0ff;
+      } /* Literal.Number.Integer.Long */
+      .highlight .p {
+        color: #8b949e;
+      } /* Punctuation */
+      .highlight .x {
+        color: #c9d1d9;
+      } /* Other */
+
+      /* ==================== Footer Styles ==================== */
+
+      .page-footer {
+        margin-top: 4rem;
+        padding-top: 2rem;
+        border-top: 1px solid rgb(226 232 240); /* slate-200 */
+      }
+      .page-footer .footer-content {
+        display: flex;
+        flex-direction: column;
+        gap: 1rem;
+        color: rgb(100 116 139); /* slate-500 */
+        font-size: 0.875rem;
+      }
+      .page-footer .footer-row {
+        display: flex;
+        align-items: center;
+        gap: 0.5rem;
+        flex-wrap: wrap;
+      }
+      .page-footer a {
+        color: #0dc09d;
+        text-decoration: none;
+      }
+      .page-footer a:hover {
+        text-decoration: underline;
+      }
+      .page-footer .nextflow-logo {
+        height: 1.25rem;
+        width: auto;
+      }
+      .page-footer a.footer-logo-link {
+        color: inherit;
+      }
+      .page-footer .nf-docs-version {
+        font-family: ui-monospace, monospace;
+        font-size: 0.75rem;
+        background-color: rgb(241 245 249); /* slate-100 */
+        padding: 0.125rem 0.375rem;
+        border-radius: 0.25rem;
+      }
+
+      /* Dark mode footer */
+      html.dark .page-footer {
+        border-top-color: rgb(51 65 85); /* slate-700 */
+      }
+      html.dark .page-footer .footer-content {
+        color: rgb(148 163 184); /* slate-400 */
+      }
+      html.dark .page-footer .nf-docs-version {
+        background-color: rgb(51 65 85); /* slate-700 */
+      }
+    </style>
+  <script src="https://cdn.tailwindcss.com"></script>
+    <script>
+      tailwind.config = {
+        theme: {
+          extend: {
+            colors: {
+              primary: {
+                DEFAULT: "#0DC09D",
+                light: "#E6F9F5",
+                dark: "#0A9A7D",
+              },
+            },
+          },
+        },
+      };
+    </script>
+</head>
+  <body class="font-sans leading-relaxed text-slate-800 bg-slate-50">
+    <!-- Top Navigation Bar -->
+    <header
+      class="fixed top-0 left-0 right-0 h-14 bg-white border-b border-slate-200 z-50 flex items-center px-4 md:px-6"
+    >
+      <!-- Mobile menu button -->
+      <button
+        id="mobile-menu-btn"
+        class="md:hidden mr-3 p-1.5 rounded hover:bg-slate-100 transition-colors"
+        aria-label="Open menu"
+      >
+        <svg class="w-6 h-6 text-slate-600" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+          <path
+            stroke-linecap="round"
+            stroke-linejoin="round"
+            stroke-width="2"
+            d="M4 6h16M4 12h16M4 18h16"
+          ></path>
+        </svg>
+      </button>
+
+      <!-- Left: Organization/user avatar (GitHub only) and pipeline name -->
+      <a
+        href="#overview"
+        id="top-nav-home"
+        class="flex items-center hover:opacity-80 transition-opacity"
+      >
+        
+        <img
+          id="repo-avatar"
+          src="data:image/png;base64,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"
+          alt="Organization avatar"
+          class="w-6 h-6 rounded mr-2"
+        />
+        
+        <h1 class="text-lg font-bold text-primary">nf-fgsv workflow parameters</h1>
+        
+        <span class="ml-2 text-sm text-slate-500"
+          >v0.1.0</span
+        >
+        
+      </a>
+
+      <!-- Right: Search and GitHub link -->
+      <div class="ml-auto flex items-center gap-4">
+        <!-- Search (hidden on mobile, shown in mobile menu) -->
+        <div class="relative hidden md:block">
+          <input
+            type="text"
+            id="search-input"
+            placeholder="Search..."
+            class="w-48 md:w-64 px-3 py-1.5 text-sm border border-slate-300 rounded-md focus:outline-none focus:ring-2 focus:ring-primary focus:border-transparent"
+          />
+          <button
+            id="search-clear"
+            class="absolute right-2 top-1/2 -translate-y-1/2 text-slate-400 hover:text-slate-600 hidden"
+            title="Clear search"
+          >
+            <svg class="w-4 h-4" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+              <path
+                stroke-linecap="round"
+                stroke-linejoin="round"
+                stroke-width="2"
+                d="M6 18L18 6M6 6l12 12"
+              ></path>
+            </svg>
+          </button>
+        </div>
+
+        <!-- Dark mode toggle -->
+        <button
+          id="theme-toggle"
+          class="theme-toggle"
+          title="Toggle dark mode"
+          aria-label="Toggle dark mode"
+        >
+          <!-- Sun icon (shown in dark mode) -->
+          <svg class="icon-sun" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+            <path
+              stroke-linecap="round"
+              stroke-linejoin="round"
+              stroke-width="2"
+              d="M12 3v1m0 16v1m9-9h-1M4 12H3m15.364 6.364l-.707-.707M6.343 6.343l-.707-.707m12.728 0l-.707.707M6.343 17.657l-.707.707M16 12a4 4 0 11-8 0 4 4 0 018 0z"
+            ></path>
+          </svg>
+          <!-- Moon icon (shown in light mode) -->
+          <svg class="icon-moon" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+            <path
+              stroke-linecap="round"
+              stroke-linejoin="round"
+              stroke-width="2"
+              d="M20.354 15.354A9 9 0 018.646 3.646 9.003 9.003 0 0012 21a9.003 9.003 0 008.354-5.646z"
+            ></path>
+          </svg>
+        </button>
+
+        <!-- Repository link -->
+        
+        <a
+          href="https://github.com/fulcrumgenomics/nf-fgsv"
+          target="_blank"
+          rel="noopener noreferrer"
+          class="flex items-center gap-1.5 text-sm text-slate-600 hover:text-primary transition-colors"
+          title="View repository"
+        >
+          
+          <!-- GitHub icon -->
+          <svg class="w-5 h-5" fill="currentColor" viewBox="0 0 24 24">
+            <path
+              fill-rule="evenodd"
+              clip-rule="evenodd"
+              d="M12 2C6.477 2 2 6.484 2 12.017c0 4.425 2.865 8.18 6.839 9.504.5.092.682-.217.682-.483 0-.237-.008-.868-.013-1.703-2.782.605-3.369-1.343-3.369-1.343-.454-1.158-1.11-1.466-1.11-1.466-.908-.62.069-.608.069-.608 1.003.07 1.531 1.032 1.531 1.032.892 1.53 2.341 1.088 2.91.832.092-.647.35-1.088.636-1.338-2.22-.253-4.555-1.113-4.555-4.951 0-1.093.39-1.988 1.029-2.688-.103-.253-.446-1.272.098-2.65 0 0 .84-.27 2.75 1.026A9.564 9.564 0 0112 6.844c.85.004 1.705.115 2.504.337 1.909-1.296 2.747-1.027 2.747-1.027.546 1.379.202 2.398.1 2.651.64.7 1.028 1.595 1.028 2.688 0 3.848-2.339 4.695-4.566 4.943.359.309.678.92.678 1.855 0 1.338-.012 2.419-.012 2.747 0 .268.18.58.688.482A10.019 10.019 0 0022 12.017C22 6.484 17.522 2 12 2z"
+            ></path>
+          </svg>
+          <span class="hidden sm:inline">GitHub</span>
+          
+        </a>
+        
+      </div>
+    </header>
+
+    <!-- Mobile Navigation Drawer -->
+    <div
+      id="mobile-menu-overlay"
+      class="fixed inset-0 bg-black/50 z-40 hidden md:hidden"
+      aria-hidden="true"
+    ></div>
+    <aside
+      id="mobile-menu"
+      class="fixed top-0 left-0 h-full w-72 bg-white z-50 transform -translate-x-full transition-transform duration-300 ease-in-out md:hidden shadow-xl"
+    >
+      <div class="flex items-center justify-between p-4 border-b border-slate-200">
+        <span class="font-bold text-primary">nf-fgsv workflow parameters</span>
+        <button
+          id="mobile-menu-close"
+          class="p-1.5 rounded hover:bg-slate-100"
+          aria-label="Close menu"
+        >
+          <svg class="w-5 h-5 text-slate-600" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+            <path
+              stroke-linecap="round"
+              stroke-linejoin="round"
+              stroke-width="2"
+              d="M6 18L18 6M6 6l12 12"
+            ></path>
+          </svg>
+        </button>
+      </div>
+
+      <!-- Mobile Navigation Links -->
+      <div id="mobile-main-nav">
+        <nav class="p-4 border-b border-slate-200">
+          <!-- Search link for mobile -->
+          <a
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+                class="mobile-nav-link block px-3 py-2 rounded transition-colors hover:bg-slate-100 text-slate-800"
+                data-section="overview"
+                >Overview</a
+              >
+            </li>
+
+            
+            <li>
+              <a
+                href="#inputs"
+                class="mobile-nav-link block px-3 py-2 rounded transition-colors hover:bg-slate-100 text-slate-800"
+                data-section="inputs"
+                >Parameters</a
+              >
+            </li>
+              
+            <li>
+              <a
+                href="#workflows"
+                class="mobile-nav-link block px-3 py-2 rounded transition-colors hover:bg-slate-100 text-slate-800"
+                data-section="workflows"
+                >Workflows</a
+              >
+            </li>
+             
+            <li>
+              <a
+                href="#processes"
+                class="mobile-nav-link block px-3 py-2 rounded transition-colors hover:bg-slate-100 text-slate-800"
+                data-section="processes"
+                >Processes</a
+              >
+            </li>
+             
+          </ul>
+
+          
+          <div class="mt-6 pt-4 border-t border-slate-200">
+            <a
+              href="https://github.com/fulcrumgenomics/nf-fgsv"
+              target="_blank"
+              rel="noopener noreferrer"
+              class="flex items-center gap-2 px-3 py-2 text-sm text-slate-600 hover:text-primary transition-colors"
+            >
+              
+              <svg class="w-5 h-5" fill="currentColor" viewBox="0 0 24 24">
+                <path
+                  fill-rule="evenodd"
+                  clip-rule="evenodd"
+                  d="M12 2C6.477 2 2 6.484 2 12.017c0 4.425 2.865 8.18 6.839 9.504.5.092.682-.217.682-.483 0-.237-.008-.868-.013-1.703-2.782.605-3.369-1.343-3.369-1.343-.454-1.158-1.11-1.466-1.11-1.466-.908-.62.069-.608.069-.608 1.003.07 1.531 1.032 1.531 1.032.892 1.53 2.341 1.088 2.91.832.092-.647.35-1.088.636-1.338-2.22-.253-4.555-1.113-4.555-4.951 0-1.093.39-1.988 1.029-2.688-.103-.253-.446-1.272.098-2.65 0 0 .84-.27 2.75 1.026A9.564 9.564 0 0112 6.844c.85.004 1.705.115 2.504.337 1.909-1.296 2.747-1.027 2.747-1.027.546 1.379.202 2.398.1 2.651.64.7 1.028 1.595 1.028 2.688 0 3.848-2.339 4.695-4.566 4.943.359.309.678.92.678 1.855 0 1.338-.012 2.419-.012 2.747 0 .268.18.58.688.482A10.019 10.019 0 0022 12.017C22 6.484 17.522 2 12 2z"
+                ></path>
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+              View on GitHub 
+            </a>
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+          
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+
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+            id="mobile-toc-back"
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+                stroke-linecap="round"
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+            Back to navigation
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+
+    <div class="flex min-h-screen pt-14">
+      <!-- Left Sidebar - Main Navigation -->
+      <aside
+        id="left-nav"
+        class="w-56 bg-white border-r border-slate-200 p-6 fixed top-14 h-[calc(100vh-3.5rem)] overflow-y-auto hidden md:block"
+      >
+        <nav>
+          <ul class="space-y-1">
+            <li>
+              <a
+                href="#overview"
+                class="nav-link block px-3 py-2 rounded transition-colors hover:bg-slate-100 text-slate-800 bg-primary text-white"
+                data-section="overview"
+                >Overview</a
+              >
+            </li>
+
+            
+            <li>
+              <a
+                href="#inputs"
+                class="nav-link block px-3 py-2 rounded transition-colors hover:bg-slate-100 text-slate-800"
+                data-section="inputs"
+                >Parameters</a
+              >
+            </li>
+              
+            <li>
+              <a
+                href="#workflows"
+                class="nav-link block px-3 py-2 rounded transition-colors hover:bg-slate-100 text-slate-800"
+                data-section="workflows"
+                >Workflows</a
+              >
+            </li>
+             
+            <li>
+              <a
+                href="#processes"
+                class="nav-link block px-3 py-2 rounded transition-colors hover:bg-slate-100 text-slate-800"
+                data-section="processes"
+                >Processes</a
+              >
+            </li>
+             
+          </ul>
+        </nav>
+      </aside>
+
+      <!-- Main content -->
+      <main class="md:ml-56 lg:mr-64 flex-1 p-4 md:p-8 lg:p-12">
+        <!-- Search Results Section (hidden by default) -->
+        <section id="search-results" class="section hidden">
+          <h1 class="text-3xl font-bold mb-4 text-slate-800">Search Results</h1>
+
+          <!-- Mobile search input (visible only on mobile) -->
+          <div class="md:hidden mb-4">
+            <div class="relative">
+              <input
+                type="text"
+                id="mobile-search-input"
+                placeholder="Search..."
+                class="w-full px-3 py-2 text-sm border border-slate-300 rounded-md focus:outline-none focus:ring-2 focus:ring-primary focus:border-transparent"
+              />
+              <button
+                id="mobile-search-clear"
+                class="absolute right-2 top-1/2 -translate-y-1/2 text-slate-400 hover:text-slate-600 hidden"
+                title="Clear search"
+              >
+                <svg class="w-4 h-4" fill="none" stroke="currentColor" viewBox="0 0 24 24">
+                  <path
+                    stroke-linecap="round"
+                    stroke-linejoin="round"
+                    stroke-width="2"
+                    d="M6 18L18 6M6 6l12 12"
+                  ></path>
+                </svg>
+              </button>
+            </div>
+          </div>
+
+          <p id="search-query-wrapper" class="mb-4 text-slate-600 hidden">
+            Showing results for "<span id="search-query-display" class="font-semibold"></span>"
+          </p>
+
+          <div id="search-empty-state" class="py-8 text-center text-slate-500">
+            <svg
+              class="w-12 h-12 mx-auto mb-4 text-slate-300"
+              fill="none"
+              stroke="currentColor"
+              viewBox="0 0 24 24"
+            >
+              <path
+                stroke-linecap="round"
+                stroke-linejoin="round"
+                stroke-width="2"
+                d="M21 21l-6-6m2-5a7 7 0 11-14 0 7 7 0 0114 0z"
+              ></path>
+            </svg>
+            <p class="text-lg">Enter a search term</p>
+            <p class="text-sm mt-2">Find parameters, processes, workflows, and more</p>
+          </div>
+
+          <div id="search-results-content">
+            <!-- Results will be populated by JavaScript -->
+          </div>
+
+          <div id="search-no-results" class="hidden py-8 text-center text-slate-500">
+            <p class="text-lg">No results found</p>
+            <p class="text-sm mt-2">Try a different search term</p>
+          </div>
+        </section>
+
+        <!-- Overview Section -->
+        <section id="overview" class="section">
+          <h1 class="text-3xl font-bold mb-4 text-slate-800">nf-fgsv workflow parameters</h1>
+
+          
+          <div class="prose mb-6 text-slate-600"><p>Nextflow workflow for running fgsv.</p></div>
+           
+          <div class="flex flex-wrap gap-4 mb-6">
+             
+            <a
+              href="https://github.com/fulcrumgenomics/nf-fgsv"
+              target="_blank"
+              class="inline-flex items-center gap-1.5 text-sm text-primary hover:underline"
+            >
+              
+              <svg class="w-4 h-4 flex-shrink-0" fill="currentColor" viewBox="0 0 24 24">
+                <path
+                  fill-rule="evenodd"
+                  clip-rule="evenodd"
+                  d="M12 2C6.477 2 2 6.484 2 12.017c0 4.425 2.865 8.18 6.839 9.504.5.092.682-.217.682-.483 0-.237-.008-.868-.013-1.703-2.782.605-3.369-1.343-3.369-1.343-.454-1.158-1.11-1.466-1.11-1.466-.908-.62.069-.608.069-.608 1.003.07 1.531 1.032 1.531 1.032.892 1.53 2.341 1.088 2.91.832.092-.647.35-1.088.636-1.338-2.22-.253-4.555-1.113-4.555-4.951 0-1.093.39-1.988 1.029-2.688-.103-.253-.446-1.272.098-2.65 0 0 .84-.27 2.75 1.026A9.564 9.564 0 0112 6.844c.85.004 1.705.115 2.504.337 1.909-1.296 2.747-1.027 2.747-1.027.546 1.379.202 2.398.1 2.651.64.7 1.028 1.595 1.028 2.688 0 3.848-2.339 4.695-4.566 4.943.359.309.678.92.678 1.855 0 1.338-.012 2.419-.012 2.747 0 .268.18.58.688.482A10.019 10.019 0 0022 12.017C22 6.484 17.522 2 12 2z"
+                ></path>
+              </svg>
+               https://github.com/fulcrumgenomics/nf-fgsv
+            </a>
+            
+          </div>
+           
+          <div id="readme-content" class="prose max-w-none text-slate-600">
+            <div class="alert alert-note"><div class="alert-title"><svg class="alert-icon" viewBox="0 0 16 16" width="16" height="16"><path d="M0 8a8 8 0 1 1 16 0A8 8 0 0 1 0 8Zm8-6.5a6.5 6.5 0 1 0 0 13 6.5 6.5 0 0 0 0-13ZM6.5 7.75A.75.75 0 0 1 7.25 7h1a.75.75 0 0 1 .75.75v2.75h.25a.75.75 0 0 1 0 1.5h-2a.75.75 0 0 1 0-1.5h.25v-2h-.25a.75.75 0 0 1-.75-.75ZM8 6a1 1 0 1 1 0-2 1 1 0 0 1 0 2Z"></path></svg><span>Note</span></div><div class="alert-content"><p>This repository is primarily for testing the latest Nextflow features and the workflow is relatively simple.</p></div></div>
+<p>This is a Nextflow workflow for running <a href="https://github.com/fulcrumgenomics/fgsv">fgsv</a> on a BAM file to gather evidence for structural variation via breakpoint detection.</p>
+<h2 id="readme-set-up-environment" class="heading-anchor">Set up Environment<a href="#readme-set-up-environment" class="paragraph-link">¶</a></h2>
+<p>Make sure <a href="https://pixi.sh/latest/#installation">Pixi</a> and <a href="https://docs.docker.com/engine/install/">Docker</a> are installed.</p>
+<p>The environment for this analysis is in <a href="pixi.toml">pixi.toml</a> and is named <code>nf-fgsv</code>.</p>
+<p>To install:</p>
+<div class="highlight"><pre><span></span><code><span class="go">pixi install</span>
+</code></pre></div>
+
+<h2 id="readme-run-the-workflow" class="heading-anchor">Run the Workflow<a href="#readme-run-the-workflow" class="paragraph-link">¶</a></h2>
+<p>To save on typing, a pixi task is available which aliases <code>nextflow run main.nf</code>.</p>
+<div class="highlight"><pre><span></span><code><span class="go">pixi run \</span>
+<span class="go">    nf-workflow \</span>
+<span class="go">        -profile &quot;local,docker&quot; \</span>
+<span class="go">        --input tests/data/basic_input.tsv</span>
+</code></pre></div>
+
+<h2 id="readme-available-execution-profiles" class="heading-anchor">Available Execution Profiles<a href="#readme-available-execution-profiles" class="paragraph-link">¶</a></h2>
+<p>Several default profiles are available:</p>
+<ul>
+<li><code>local</code> limits the resources used by the workflow to (hopefully) reasonable levels</li>
+<li><code>docker</code> specifies docker containers should be used for process execution</li>
+<li><code>linux</code> adds <code>--user root</code> to docker <code>runOptions</code></li>
+</ul>
+<h2 id="readme-inputs" class="heading-anchor">Inputs<a href="#readme-inputs" class="paragraph-link">¶</a></h2>
+<p>A full description of input parameters is available using the workflow <code>--help</code> parameter, <code>pixi run nf-workflow --help</code>.</p>
+<p>The required columns in the <code>--input</code> samplesheet are:</p>
+<table>
+<thead>
+<tr>
+<th>Field</th>
+<th>Type</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>sample</code></td>
+<td>String, no whitespace</td>
+<td>Sample identifier</td>
+</tr>
+<tr>
+<td><code>bam</code></td>
+<td>Absolute path</td>
+<td>Path to the BAM file for this sample (may be an AWS S3 path)</td>
+</tr>
+</tbody>
+</table>
+<h3 id="readme-parameter-files" class="heading-anchor">Parameter files<a href="#readme-parameter-files" class="paragraph-link">¶</a></h3>
+<p>If using more than a few parameters, consider saving them in a YAML format file (e.g. <a href="tests/integration/params.yml">tests/integration/params.yml</a>).</p>
+<div class="highlight"><pre><span></span><code><span class="go">pixi run \</span>
+<span class="go">    nf-workflow \</span>
+<span class="go">        -profile &quot;local,docker&quot; \</span>
+<span class="go">        -params-file my_params.yml</span>
+</code></pre></div>
+
+<h2 id="readme-outputs" class="heading-anchor">Outputs<a href="#readme-outputs" class="paragraph-link">¶</a></h2>
+<p>The output directory can be specified using the <code>-output-dir</code> Nextflow parameter.
+The default output directory is <code>results/</code>.
+<code>-output-dir</code> cannot be specified in a <code>params.yml</code> file, because it is a Nextflow parameter rather than a workflow parameter.
+It must be specified on the command line or in a <code>nextflow.config</code> file.</p>
+<div class="highlight"><pre><span></span><code><span class="go">pixi run \</span>
+<span class="go">    nf-workflow \</span>
+<span class="go">        -profile &quot;local,docker&quot; \</span>
+<span class="go">        --input tests/data/basic_input.tsv \</span>
+<span class="go">        -output-dir results</span>
+</code></pre></div>
+
+<details>
+<summary>Click to toggle output directory structure</summary>
+
+
+
+<div class="highlight"><pre><span></span><code><span class="go">results</span>
+<span class="go">└── {sample_name}</span>
+<span class="go">    ├── {sample_name}_sorted.bam                # Coordinate-sorted BAM file</span>
+<span class="go">    ├── {sample_name}_svpileup.txt              # SvPileup breakpoint candidates</span>
+<span class="go">    ├── {sample_name}_svpileup.bam              # BAM with SV tags from SvPileup</span>
+<span class="go">    ├── {sample_name}_svpileup.aggregate.txt    # Aggregated/merged breakpoint pileups</span>
+<span class="go">    └── {sample_name}_svpileup.aggregate.bedpe  # Aggregated pileups in BEDPE format</span>
+</code></pre></div>
+
+
+
+</details>
+
+<h3 id="readme-output-file-descriptions" class="heading-anchor">Output File Descriptions<a href="#readme-output-file-descriptions" class="paragraph-link">¶</a></h3>
+<table>
+<thead>
+<tr>
+<th>File</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>*_sorted.bam</code></td>
+<td>Input BAM sorted by genomic coordinates using samtools sort</td>
+</tr>
+<tr>
+<td><code>*_svpileup.txt</code></td>
+<td>Candidate structural variant breakpoints identified by <a href="https://github.com/fulcrumgenomics/fgsv">fgsv SvPileup</a></td>
+</tr>
+<tr>
+<td><code>*_svpileup.bam</code></td>
+<td>BAM file with SV-related tags added by SvPileup</td>
+</tr>
+<tr>
+<td><code>*_svpileup.aggregate.txt</code></td>
+<td>Merged breakpoint pileups from <a href="https://github.com/fulcrumgenomics/fgsv">fgsv AggregateSvPileup</a></td>
+</tr>
+<tr>
+<td><code>*_svpileup.aggregate.bedpe</code></td>
+<td>Aggregated pileups converted to <a href="https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format">BEDPE format</a></td>
+</tr>
+</tbody>
+</table>
+<h2 id="readme-contributing" class="heading-anchor">Contributing<a href="#readme-contributing" class="paragraph-link">¶</a></h2>
+<p>See our <a href="docs/CONTRIBUTING.md">Contributing Guide</a> for development and testing guidelines.</p>
+          </div>
+           
+          <h2 class="text-2xl font-semibold mt-8 mb-4 pb-2 border-b border-slate-200">Authors</h2>
+          <ul class="list-disc list-inside mb-4">
+            
+            <li>Fulcrum Genomics</li>
+            
+          </ul>
+          
+        </section>
+
+        <!-- Inputs Section -->
+        <section id="inputs" class="section hidden">
+          <h1 class="text-3xl font-bold mb-4 text-slate-800">Pipeline Inputs</h1>
+          <p class="mb-4 text-slate-600">
+            This page documents all input parameters for the pipeline.
+          </p>
+
+          
+          <h2
+            id="inputs-main-workflow-parameters"
+            class="text-2xl font-semibold mt-8 mb-4 pb-2 border-b border-slate-200 heading-anchor"
+          >
+            Main workflow parameters
+            <a href="#inputs-main-workflow-parameters" class="paragraph-link">¶</a>
+          </h2>
+
+          
+          <div
+            id="param-input"
+            class="mb-6 pb-6 border-b border-slate-200 last:border-b-0"
+          >
+            <div class="font-mono font-semibold text-lg heading-anchor">
+              --input
+              <a href="#param-input" class="paragraph-link">¶</a>
+            </div>
+            <div class="flex flex-wrap gap-2 my-2">
+              <span
+                class="inline-block px-2 py-0.5 rounded-full text-xs font-medium bg-purple-100 text-purple-700"
+              >
+                string
+              </span>
+              
+              <span
+                class="inline-block px-2 py-0.5 rounded-full text-xs font-medium bg-purple-100 text-purple-700"
+              >
+                file-path
+              </span>
+               
+              <span
+                class="inline-block px-2 py-0.5 rounded-full text-xs font-medium bg-yellow-100 text-yellow-800"
+              >
+                Pattern: <code class="font-mono">.*.tsv$</code>
+              </span>
+               
+              <span
+                class="inline-block px-2 py-0.5 rounded-full text-xs font-medium bg-red-100 text-red-600"
+              >
+                Required
+              </span>
+              
+            </div>
+            
+            <div class="prose mb-2 text-slate-600"><p>Path to tab-separated file containing information about the samples in the experiment.</p></div>
+               
+          </div>
+           
+        </section>
+
+        <!-- Config Section -->
+        
+
+        <!-- Workflows Section -->
+        
+        <section id="workflows" class="section hidden">
+          <h1 class="text-3xl font-bold mb-4 text-slate-800">Workflows</h1>
+          <p class="mb-4 text-slate-600">This page documents all workflows in the pipeline.</p>
+
+          
+          <div
+            id="workflow-entry"
+            class="bg-white border border-slate-200 rounded-lg p-4 mb-4"
+          >
+            <!-- Signature header like Sphinx API docs -->
+            <div
+              class="bg-slate-100 border-l-4 border-primary px-4 py-2 mb-4 font-mono text-sm heading-anchor"
+            >
+              <span class="text-slate-500 italic">workflow</span>
+              <span class="font-bold text-primary-dark">&lt;entry&gt;</span>
+              
+              <span
+                class="ml-2 inline-block px-2 py-0.5 rounded-full text-xs font-medium bg-green-100 text-green-700"
+              >
+                Entry Point
+              </span>
+               
+              <a
+                href="https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/main.nf#L19-L42"
+                target="_blank"
+                rel="noopener noreferrer"
+                class="ml-2 text-slate-400 hover:text-primary no-underline"
+                title="View source code"
+                >[source]</a
+              >
+              
+              <a href="#workflow-entry" class="paragraph-link">¶</a>
+            </div>
+            
+            <div class="text-xs text-slate-400 mb-2">
+              Defined in <code>main.nf:19</code>
+            </div>
+            
+
+            <!-- Keywords badges (from meta.yml) -->
+            
+
+            <!-- meta.yml description (if present) -->
+            
+
+            <!-- Code documentation (Groovydoc) - show if present and different from meta description -->
+            
+
+            <!-- Components section (from meta.yml - modules/subworkflows used) -->
+            
+
+            <!-- Inputs section - combine LSP inputs with meta.yml descriptions -->
+            
+
+            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
+             
+
+            <!-- Authors/Maintainers (from meta.yml) -->
+            
+          </div>
+          
+        </section>
+        
+
+        <!-- Processes Section -->
+        
+        <section id="processes" class="section hidden">
+          <h1 class="text-3xl font-bold mb-4 text-slate-800">Processes</h1>
+          <p class="mb-4 text-slate-600">This page documents all processes in the pipeline.</p>
+
+          
+          <div
+            id="process-AGGREGATE_SV_PILEUP"
+            class="bg-white border border-slate-200 rounded-lg p-4 mb-4"
+          >
+            <!-- Signature header like Sphinx API docs -->
+            <div
+              class="bg-slate-100 border-l-4 border-primary px-4 py-2 mb-4 font-mono text-sm heading-anchor"
+            >
+              <span class="text-slate-500 italic">process</span>
+              <span class="font-bold text-primary-dark">AGGREGATE_SV_PILEUP</span>
+              
+              <a
+                href="https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/aggregate_sv_pileup.nf#L12-L33"
+                target="_blank"
+                rel="noopener noreferrer"
+                class="ml-2 text-slate-400 hover:text-primary no-underline"
+                title="View source code"
+                >[source]</a
+              >
+               
+              <a href="#process-AGGREGATE_SV_PILEUP" class="paragraph-link">¶</a>
+            </div>
+            
+            <div class="text-xs text-slate-400 mb-2">
+              Defined in <code>modules/aggregate_sv_pileup.nf:12</code>
+            </div>
+            
+
+            <!-- Keywords badges (from meta.yml) -->
+            
+
+            <!-- meta.yml description (if present) -->
+            
+
+            <!-- Code documentation (Groovydoc) - show if present and different from meta description -->
+             
+            <div class="prose mb-4 text-slate-600"><p>Aggregate and merge pileups that are likely to support the same breakpoint
+using fgsv AggregateSvPileup.</p></div>
+            
+
+            <!-- Tools section (from meta.yml) -->
+            
+
+            <!-- Inputs section - combine LSP inputs with meta.yml descriptions -->
+            
+            <h3 class="text-lg font-semibold mt-4 mb-2">Inputs</h3>
+            <div class="overflow-x-auto">
+              <table class="w-full border-collapse mb-4">
+                <thead>
+                  <tr>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Name
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Type
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Description
+                    </th>
+                  </tr>
+                </thead>
+                <tbody>
+                    
+                  <tr class="hover:bg-slate-50">
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >val(meta)<wbr>,<wbr> <wbr>path(bam)<wbr>,<wbr> <wbr>path(txt)<wbr></code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >tuple</code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <div class="prose prose-sm"><p><code>meta</code>: Map containing sample information (must include 'id'); <code>bam</code>: Input BAM file; <code>txt</code>: SvPileup breakpoint output file</p></div>
+                      
+                    </td>
+                  </tr>
+                   
+                </tbody>
+              </table>
+            </div>
+            
+
+            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
+            
+            <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
+            <div class="overflow-x-auto">
+              <table class="w-full border-collapse mb-4">
+                <thead>
+                  <tr>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Name
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Type
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Emit
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Description
+                    </th>
+                  </tr>
+                </thead>
+                <tbody>
+                    
+                  <tr class="hover:bg-slate-50">
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >val(meta)<wbr>,<wbr> <wbr>file("*_svpileup.aggregate.txt")<wbr></code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >tuple</code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >txt</code
+                      >
+                      
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <div class="prose prose-sm"><p>Tuple of meta and aggregated SvPileup output file</p></div>
+                      
+                    </td>
+                  </tr>
+                   
+                </tbody>
+              </table>
+            </div>
+             
+
+            <!-- Authors/Maintainers (from meta.yml) -->
+            
+          </div>
+          
+          <div
+            id="process-AGGREGATE_SV_PILEUP_TO_BEDPE"
+            class="bg-white border border-slate-200 rounded-lg p-4 mb-4"
+          >
+            <!-- Signature header like Sphinx API docs -->
+            <div
+              class="bg-slate-100 border-l-4 border-primary px-4 py-2 mb-4 font-mono text-sm heading-anchor"
+            >
+              <span class="text-slate-500 italic">process</span>
+              <span class="font-bold text-primary-dark">AGGREGATE_SV_PILEUP_TO_BEDPE</span>
+              
+              <a
+                href="https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/aggregate_sv_pileup_to_bedpe.nf#L11-L31"
+                target="_blank"
+                rel="noopener noreferrer"
+                class="ml-2 text-slate-400 hover:text-primary no-underline"
+                title="View source code"
+                >[source]</a
+              >
+               
+              <a href="#process-AGGREGATE_SV_PILEUP_TO_BEDPE" class="paragraph-link">¶</a>
+            </div>
+            
+            <div class="text-xs text-slate-400 mb-2">
+              Defined in <code>modules/aggregate_sv_pileup_to_bedpe.nf:11</code>
+            </div>
+            
+
+            <!-- Keywords badges (from meta.yml) -->
+            
+
+            <!-- meta.yml description (if present) -->
+            
+
+            <!-- Code documentation (Groovydoc) - show if present and different from meta description -->
+             
+            <div class="prose mb-4 text-slate-600"><p>Convert aggregated SvPileup output to BEDPE format using fgsv
+AggregateSvPileupToBedPE.</p></div>
+            
+
+            <!-- Tools section (from meta.yml) -->
+            
+
+            <!-- Inputs section - combine LSP inputs with meta.yml descriptions -->
+            
+            <h3 class="text-lg font-semibold mt-4 mb-2">Inputs</h3>
+            <div class="overflow-x-auto">
+              <table class="w-full border-collapse mb-4">
+                <thead>
+                  <tr>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Name
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Type
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Description
+                    </th>
+                  </tr>
+                </thead>
+                <tbody>
+                    
+                  <tr class="hover:bg-slate-50">
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >val(meta)<wbr>,<wbr> <wbr>path(txt)<wbr></code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >tuple</code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <div class="prose prose-sm"><p><code>meta</code>: Map containing sample information (must include 'id'); <code>txt</code>: Aggregated SvPileup output file</p></div>
+                      
+                    </td>
+                  </tr>
+                   
+                </tbody>
+              </table>
+            </div>
+            
+
+            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
+            
+            <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
+            <div class="overflow-x-auto">
+              <table class="w-full border-collapse mb-4">
+                <thead>
+                  <tr>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Name
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Type
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Emit
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Description
+                    </th>
+                  </tr>
+                </thead>
+                <tbody>
+                    
+                  <tr class="hover:bg-slate-50">
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >val(meta)<wbr>,<wbr> <wbr>file("*_svpileup.aggregate.bedpe")<wbr></code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >tuple</code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >bedpe</code
+                      >
+                      
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <div class="prose prose-sm"><p>Tuple of meta and BEDPE format output file</p></div>
+                      
+                    </td>
+                  </tr>
+                   
+                </tbody>
+              </table>
+            </div>
+             
+
+            <!-- Authors/Maintainers (from meta.yml) -->
+            
+          </div>
+          
+          <div
+            id="process-COORDINATE_SORT"
+            class="bg-white border border-slate-200 rounded-lg p-4 mb-4"
+          >
+            <!-- Signature header like Sphinx API docs -->
+            <div
+              class="bg-slate-100 border-l-4 border-primary px-4 py-2 mb-4 font-mono text-sm heading-anchor"
+            >
+              <span class="text-slate-500 italic">process</span>
+              <span class="font-bold text-primary-dark">COORDINATE_SORT</span>
+              
+              <a
+                href="https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/coordinate_sort.nf#L10-L31"
+                target="_blank"
+                rel="noopener noreferrer"
+                class="ml-2 text-slate-400 hover:text-primary no-underline"
+                title="View source code"
+                >[source]</a
+              >
+               
+              <a href="#process-COORDINATE_SORT" class="paragraph-link">¶</a>
+            </div>
+            
+            <div class="text-xs text-slate-400 mb-2">
+              Defined in <code>modules/coordinate_sort.nf:10</code>
+            </div>
+            
+
+            <!-- Keywords badges (from meta.yml) -->
+            
+
+            <!-- meta.yml description (if present) -->
+            
+
+            <!-- Code documentation (Groovydoc) - show if present and different from meta description -->
+             
+            <div class="prose mb-4 text-slate-600"><p>Sort a BAM file by genomic coordinates using samtools sort.</p></div>
+            
+
+            <!-- Tools section (from meta.yml) -->
+            
+
+            <!-- Inputs section - combine LSP inputs with meta.yml descriptions -->
+            
+            <h3 class="text-lg font-semibold mt-4 mb-2">Inputs</h3>
+            <div class="overflow-x-auto">
+              <table class="w-full border-collapse mb-4">
+                <thead>
+                  <tr>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Name
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Type
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Description
+                    </th>
+                  </tr>
+                </thead>
+                <tbody>
+                    
+                  <tr class="hover:bg-slate-50">
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >val(meta)<wbr>,<wbr> <wbr>path(bam)<wbr></code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >tuple</code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <div class="prose prose-sm"><p><code>meta</code>: Map containing sample information (must include 'id'); <code>bam</code>: Input BAM file to be sorted</p></div>
+                      
+                    </td>
+                  </tr>
+                   
+                </tbody>
+              </table>
+            </div>
+            
+
+            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
+            
+            <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
+            <div class="overflow-x-auto">
+              <table class="w-full border-collapse mb-4">
+                <thead>
+                  <tr>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Name
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Type
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Emit
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Description
+                    </th>
+                  </tr>
+                </thead>
+                <tbody>
+                    
+                  <tr class="hover:bg-slate-50">
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >val(meta)<wbr>,<wbr> <wbr>file("*_sorted.bam")<wbr></code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >tuple</code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >bam</code
+                      >
+                      
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <div class="prose prose-sm"><p>Tuple of meta and coordinate-sorted BAM file</p></div>
+                      
+                    </td>
+                  </tr>
+                   
+                </tbody>
+              </table>
+            </div>
+             
+
+            <!-- Authors/Maintainers (from meta.yml) -->
+            
+          </div>
+          
+          <div
+            id="process-SV_PILEUP"
+            class="bg-white border border-slate-200 rounded-lg p-4 mb-4"
+          >
+            <!-- Signature header like Sphinx API docs -->
+            <div
+              class="bg-slate-100 border-l-4 border-primary px-4 py-2 mb-4 font-mono text-sm heading-anchor"
+            >
+              <span class="text-slate-500 italic">process</span>
+              <span class="font-bold text-primary-dark">SV_PILEUP</span>
+              
+              <a
+                href="https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/sv_pileup.nf#L11-L33"
+                target="_blank"
+                rel="noopener noreferrer"
+                class="ml-2 text-slate-400 hover:text-primary no-underline"
+                title="View source code"
+                >[source]</a
+              >
+               
+              <a href="#process-SV_PILEUP" class="paragraph-link">¶</a>
+            </div>
+            
+            <div class="text-xs text-slate-400 mb-2">
+              Defined in <code>modules/sv_pileup.nf:11</code>
+            </div>
+            
+
+            <!-- Keywords badges (from meta.yml) -->
+            
+
+            <!-- meta.yml description (if present) -->
+            
+
+            <!-- Code documentation (Groovydoc) - show if present and different from meta description -->
+             
+            <div class="prose mb-4 text-slate-600"><p>Detect structural variant evidence from a BAM file using fgsv SvPileup.</p></div>
+            
+
+            <!-- Tools section (from meta.yml) -->
+            
+
+            <!-- Inputs section - combine LSP inputs with meta.yml descriptions -->
+            
+            <h3 class="text-lg font-semibold mt-4 mb-2">Inputs</h3>
+            <div class="overflow-x-auto">
+              <table class="w-full border-collapse mb-4">
+                <thead>
+                  <tr>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Name
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Type
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Description
+                    </th>
+                  </tr>
+                </thead>
+                <tbody>
+                    
+                  <tr class="hover:bg-slate-50">
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >val(meta)<wbr>,<wbr> <wbr>path(bam)<wbr></code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >tuple</code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <div class="prose prose-sm"><p><code>meta</code>: Map containing sample information (must include 'id'); <code>bam</code>: Input BAM file</p></div>
+                      
+                    </td>
+                  </tr>
+                   
+                </tbody>
+              </table>
+            </div>
+            
+
+            <!-- Outputs section - combine LSP outputs with meta.yml descriptions -->
+            
+            <h3 class="text-lg font-semibold mt-4 mb-2">Outputs</h3>
+            <div class="overflow-x-auto">
+              <table class="w-full border-collapse mb-4">
+                <thead>
+                  <tr>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Name
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Type
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Emit
+                    </th>
+                    <th class="text-left p-3 border-b border-slate-200 bg-slate-100 font-semibold">
+                      Description
+                    </th>
+                  </tr>
+                </thead>
+                <tbody>
+                    
+                  <tr class="hover:bg-slate-50">
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >val(meta)<wbr>,<wbr> <wbr>file("*_svpileup.txt")<wbr></code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >tuple</code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >txt</code
+                      >
+                      
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <div class="prose prose-sm"><p>Tuple of meta and SvPileup breakpoint output file</p></div>
+                      
+                    </td>
+                  </tr>
+                  
+                  <tr class="hover:bg-slate-50">
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >val(meta)<wbr>,<wbr> <wbr>file("*_svpileup.bam")<wbr></code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >tuple</code
+                      >
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <code class="bg-slate-100 px-1.5 py-0.5 rounded font-mono text-sm"
+                        >bam</code
+                      >
+                      
+                    </td>
+                    <td class="p-3 border-b border-slate-200">
+                      
+                      <div class="prose prose-sm"><p>Tuple of meta and SvPileup BAM file</p></div>
+                      
+                    </td>
+                  </tr>
+                   
+                </tbody>
+              </table>
+            </div>
+             
+
+            <!-- Authors/Maintainers (from meta.yml) -->
+            
+          </div>
+          
+        </section>
+        
+
+        <!-- Functions Section -->
+        
+
+        <!-- Page Footer -->
+        <footer class="page-footer">
+          <div class="footer-content">
+            <div class="footer-row">
+              <span>Pipeline built with</span>
+              <a
+                href="https://nextflow.io"
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+            <div class="footer-row">
+              <span>Documentation generated by</span>
+              <a href="https://github.com/ewels/nf-docs" target="_blank" rel="noopener noreferrer"
+                >nf-docs</a
+              >
+              <span class="nf-docs-version">v0.2.0</span>
+              <span>on 2026-03-03 19:13:28 UTC</span>
+            </div>
+          </div>
+        </footer>
+      </main>
+
+      <!-- Right Sidebar - Page Table of Contents -->
+      <aside
+        id="right-nav"
+        class="w-64 bg-white border-l border-slate-200 p-4 fixed right-0 top-14 h-[calc(100vh-3.5rem)] overflow-y-auto hidden lg:block"
+      >
+        <div class="text-xs font-semibold uppercase tracking-wide text-slate-500 mb-3">
+          On This Page
+        </div>
+
+        <!-- Overview TOC (empty - no sub-items) -->
+        <nav id="toc-overview" class="toc-section"></nav>
+
+        <!-- Inputs TOC -->
+        
+        <nav id="toc-inputs" class="toc-section hidden">
+          
+          <div class="mb-3">
+            <div
+              class="font-semibold text-sm text-slate-700 mb-1 toc-group-header cursor-pointer hover:text-primary"
+              data-group="main-workflow-parameters"
+            >
+              Main workflow parameters
+            </div>
+            <ul
+              class="toc-group-items space-y-0.5 text-xs"
+              data-group="main-workflow-parameters"
+            >
+              
+              <li>
+                <a
+                  href="#param-input"
+                  class="toc-link block px-2 py-0.5 rounded text-slate-600 hover:bg-slate-100 hover:text-slate-900 truncate"
+                  data-section="inputs"
+                  title="input"
+                  >input</a
+                >
+              </li>
+              
+            </ul>
+          </div>
+          
+        </nav>
+        
+
+        <!-- Config TOC -->
+        
+
+        <!-- Workflows TOC -->
+        
+        <nav id="toc-workflows" class="toc-section hidden">
+          <ul class="space-y-0.5 text-xs">
+            
+            <li>
+              <a
+                href="#workflow-entry"
+                class="toc-link block px-2 py-0.5 rounded text-slate-600 hover:bg-slate-100 hover:text-slate-900 truncate"
+                data-section="workflows"
+                title="(entry)"
+                >(entry)</a
+              >
+            </li>
+            
+          </ul>
+        </nav>
+        
+
+        <!-- Processes TOC -->
+        
+        <nav id="toc-processes" class="toc-section hidden">
+          <ul class="space-y-0.5 text-xs">
+            
+            <li>
+              <a
+                href="#process-AGGREGATE_SV_PILEUP"
+                class="toc-link block px-2 py-0.5 rounded text-slate-600 hover:bg-slate-100 hover:text-slate-900 truncate"
+                data-section="processes"
+                title="AGGREGATE_SV_PILEUP"
+                >AGGREGATE_SV_PILEUP</a
+              >
+            </li>
+            
+            <li>
+              <a
+                href="#process-AGGREGATE_SV_PILEUP_TO_BEDPE"
+                class="toc-link block px-2 py-0.5 rounded text-slate-600 hover:bg-slate-100 hover:text-slate-900 truncate"
+                data-section="processes"
+                title="AGGREGATE_SV_PILEUP_TO_BEDPE"
+                >AGGREGATE_SV_PILEUP_TO_BEDPE</a
+              >
+            </li>
+            
+            <li>
+              <a
+                href="#process-COORDINATE_SORT"
+                class="toc-link block px-2 py-0.5 rounded text-slate-600 hover:bg-slate-100 hover:text-slate-900 truncate"
+                data-section="processes"
+                title="COORDINATE_SORT"
+                >COORDINATE_SORT</a
+              >
+            </li>
+            
+            <li>
+              <a
+                href="#process-SV_PILEUP"
+                class="toc-link block px-2 py-0.5 rounded text-slate-600 hover:bg-slate-100 hover:text-slate-900 truncate"
+                data-section="processes"
+                title="SV_PILEUP"
+                >SV_PILEUP</a
+              >
+            </li>
+            
+          </ul>
+        </nav>
+        
+
+        <!-- Functions TOC -->
+        
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+    </div>
+
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+        // Escape special CSS selector characters in the ID
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+          let section = target.classList.contains('section') ? target : target.closest('.section');
+          if (section) {
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+
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+          {
+            name: "(entry)",
+            docstring: "",
+            file: "main.nf",
+            id: "workflow-entry",
+            section: "workflows"
+          }
+          
+        ],
+        processes: [
+          
+          {
+            name: "AGGREGATE_SV_PILEUP",
+            docstring: "Aggregate and merge pileups that are likely to support the same breakpoint\nusing fgsv AggregateSvPileup.",
+            file: "modules/aggregate_sv_pileup.nf",
+            id: "process-AGGREGATE_SV_PILEUP",
+            section: "processes"
+          },
+          
+          {
+            name: "AGGREGATE_SV_PILEUP_TO_BEDPE",
+            docstring: "Convert aggregated SvPileup output to BEDPE format using fgsv\nAggregateSvPileupToBedPE.",
+            file: "modules/aggregate_sv_pileup_to_bedpe.nf",
+            id: "process-AGGREGATE_SV_PILEUP_TO_BEDPE",
+            section: "processes"
+          },
+          
+          {
+            name: "COORDINATE_SORT",
+            docstring: "Sort a BAM file by genomic coordinates using samtools sort.",
+            file: "modules/coordinate_sort.nf",
+            id: "process-COORDINATE_SORT",
+            section: "processes"
+          },
+          
+          {
+            name: "SV_PILEUP",
+            docstring: "Detect structural variant evidence from a BAM file using fgsv SvPileup.",
+            file: "modules/sv_pileup.nf",
+            id: "process-SV_PILEUP",
+            section: "processes"
+          }
+          
+        ],
+        functions: [
+          
+        ],
+        inputs: [
+          
+          {
+            name: "input",
+            description: "Path to tab-separated file containing information about the samples in the experiment.",
+            group: "Main workflow parameters",
+            id: "param-input",
+            section: "inputs"
+          }
+          
+        ],
+        config: [
+          
+        ]
+      };
+
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+      const searchClear = document.getElementById('search-clear');
+      const searchResultsSection = document.getElementById('search-results');
+      const searchResultsContent = document.getElementById('search-results-content');
+      const searchNoResults = document.getElementById('search-no-results');
+      const searchQueryDisplay = document.getElementById('search-query-display');
+      const searchQueryWrapper = document.getElementById('search-query-wrapper');
+      const searchEmptyState = document.getElementById('search-empty-state');
+
+      // Debounce function
+      function debounce(func, wait) {
+        let timeout;
+        return function executedFunction(...args) {
+          const later = () => {
+            clearTimeout(timeout);
+            func(...args);
+          };
+          clearTimeout(timeout);
+          timeout = setTimeout(later, wait);
+        };
+      }
+
+      // Highlight matching text
+      function highlightText(text, query) {
+        if (!text || !query) return text || '';
+        const regex = new RegExp(`(${query.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')})`, 'gi');
+        return text.replace(regex, '<span class="search-highlight">$1</span>');
+      }
+
+      // Search function
+      function performSearch(query) {
+        if (!query || query.length < 2) {
+          // If we're on the search results page, stay there but show empty state
+          if (currentSection === 'search-results' || !searchResultsSection.classList.contains('hidden')) {
+            searchResultsContent.innerHTML = '';
+            searchNoResults.classList.add('hidden');
+            searchQueryWrapper.classList.add('hidden');
+            searchEmptyState.classList.remove('hidden');
+            searchClear.classList.add('hidden');
+            // Update URL to remove search param
+            const url = new URL(window.location);
+            url.searchParams.delete('search');
+            history.replaceState(null, null, url.pathname + url.hash);
+            return;
+          }
+          // Otherwise, show previous section
+          searchResultsSection.classList.add('hidden');
+          if (currentSection && currentSection !== 'search-results') {
+            document.getElementById(currentSection).classList.remove('hidden');
+          } else {
+            document.getElementById('overview').classList.remove('hidden');
+            currentSection = 'overview';
+            updateTOC('overview');
+          }
+          searchClear.classList.add('hidden');
+          // Update URL to remove search param
+          const url = new URL(window.location);
+          url.searchParams.delete('search');
+          history.replaceState(null, null, url.pathname + url.hash);
+          return;
+        }
+
+        searchClear.classList.remove('hidden');
+        searchEmptyState.classList.add('hidden');
+        searchQueryWrapper.classList.remove('hidden');
+        const lowerQuery = query.toLowerCase();
+        const results = {
+          workflows: [],
+          processes: [],
+          functions: [],
+          inputs: [],
+          config: []
+        };
+
+        // Search each category
+        for (const [category, items] of Object.entries(searchIndex)) {
+          for (const item of items) {
+            const nameMatch = item.name.toLowerCase().includes(lowerQuery);
+            const docMatch = (item.docstring || item.description || '').toLowerCase().includes(lowerQuery);
+            const fileMatch = (item.file || '').toLowerCase().includes(lowerQuery);
+
+            if (nameMatch || docMatch || fileMatch) {
+              results[category].push({
+                ...item,
+                nameMatch,
+                docMatch,
+                fileMatch
+              });
+            }
+          }
+        }
+
+        // Update URL with search param
+        const url = new URL(window.location);
+        url.searchParams.set('search', query);
+        history.replaceState(null, null, url.pathname + '?' + url.searchParams.toString());
+
+        // Render results
+        renderSearchResults(results, query);
+      }
+
+      // Render search results
+      function renderSearchResults(results, query) {
+        const totalResults = Object.values(results).reduce((sum, arr) => sum + arr.length, 0);
+
+        searchQueryDisplay.textContent = query;
+
+        // Hide all other sections and show search results
+        document.querySelectorAll('.section').forEach(s => s.classList.add('hidden'));
+        searchResultsSection.classList.remove('hidden');
+
+        // Clear left nav highlighting
+        document.querySelectorAll('.nav-link').forEach(l => {
+          l.classList.remove('bg-primary', 'text-white');
+          l.classList.add('text-slate-800');
+        });
+
+        // Hide right TOC
+        document.querySelectorAll('.toc-section').forEach(toc => toc.classList.add('hidden'));
+
+        if (totalResults === 0) {
+          searchResultsContent.innerHTML = '';
+          searchNoResults.classList.remove('hidden');
+          return;
+        }
+
+        searchNoResults.classList.add('hidden');
+
+        const categoryLabels = {
+          workflows: 'Workflows',
+          processes: 'Processes',
+          functions: 'Functions',
+          inputs: 'Parameters',
+          config: 'Configuration'
+        };
+
+        const categoryIcons = {
+          workflows: 'workflow',
+          processes: 'process',
+          functions: 'def',
+          inputs: '--',
+          config: ''
+        };
+
+        let html = '';
+
+        for (const [category, items] of Object.entries(results)) {
+          if (items.length === 0) continue;
+
+          html += `
+            <div class="mb-8">
+              <h2 class="text-xl font-semibold mb-4 pb-2 border-b border-slate-200">
+                ${categoryLabels[category]}
+                <span class="text-sm font-normal text-slate-500 ml-2">(${items.length})</span>
+              </h2>
+              <div class="space-y-3">
+          `;
+
+          for (const item of items) {
+            const escapedId = item.id.replace(/\./g, '\\.');
+            const icon = categoryIcons[category];
+            const description = item.docstring || item.description || '';
+            const truncatedDesc = description.length > 200 ? description.substring(0, 200) + '...' : description;
+
+            html += `
+              <div class="bg-white border border-slate-200 rounded-lg p-4 hover:border-primary transition-colors">
+                <a href="#${item.id}" class="search-result-link block" data-section="${item.section}" data-id="${item.id}">
+                  <div class="font-mono text-sm mb-1">
+                    ${icon ? `<span class="text-slate-500 italic">${icon}</span> ` : ''}
+                    <span class="font-bold text-primary-dark">${highlightText(item.name, query)}</span>
+                  </div>
+                  ${truncatedDesc ? `<p class="text-sm text-slate-600">${highlightText(truncatedDesc, query)}</p>` : ''}
+                  ${item.file ? `<p class="text-xs text-slate-400 mt-1">${highlightText(item.file, query)}</p>` : ''}
+                </a>
+              </div>
+            `;
+          }
+
+          html += `
+              </div>
+            </div>
+          `;
+        }
+
+        searchResultsContent.innerHTML = html;
+
+        // Add click handlers to search result links
+        document.querySelectorAll('.search-result-link').forEach(link => {
+          link.addEventListener('click', e => {
+            e.preventDefault();
+            const section = link.dataset.section;
+            const id = link.dataset.id;
+            const escapedId = id.replace(/\./g, '\\.');
+
+            // Clear search (input and URL)
+            const basePath = clearSearch();
+
+            // Show the target section
+            document.querySelectorAll('.section').forEach(s => s.classList.add('hidden'));
+            document.getElementById(section).classList.remove('hidden');
+            currentSection = section;
+            updateTOC(section);
+
+            // Update left nav
+            document.querySelectorAll('.nav-link').forEach(l => {
+              l.classList.remove('bg-primary', 'text-white');
+              l.classList.add('text-slate-800');
+              if (l.dataset.section === section) {
+                l.classList.add('bg-primary', 'text-white');
+                l.classList.remove('text-slate-800');
+              }
+            });
+
+            // Scroll to the item
+            const target = document.querySelector('#' + escapedId);
+            if (target) {
+              setTimeout(() => target.scrollIntoView({ behavior: 'smooth' }), 50);
+            }
+
+            // Update URL (without search params)
+            history.pushState(null, null, basePath + '#' + id);
+          });
+        });
+      }
+
+      // Debounced search
+      const debouncedSearch = debounce(performSearch, 300);
+
+      // Search input event
+      searchInput.addEventListener('input', e => {
+        debouncedSearch(e.target.value.trim());
+      });
+
+      // Clear search button
+      searchClear.addEventListener('click', () => {
+        searchInput.value = '';
+        performSearch('');
+        searchInput.focus();
+      });
+
+      // Handle search query in URL on page load
+      const urlParams = new URLSearchParams(window.location.search);
+      const searchQuery = urlParams.get('search');
+      if (searchQuery) {
+        searchInput.value = searchQuery;
+        performSearch(searchQuery);
+      }
+
+      // Keyboard shortcut: focus search with /
+      document.addEventListener('keydown', e => {
+        if (e.key === '/' && document.activeElement !== searchInput) {
+          e.preventDefault();
+          searchInput.focus();
+        }
+        // Escape to clear search
+        if (e.key === 'Escape' && document.activeElement === searchInput) {
+          searchInput.value = '';
+          performSearch('');
+          searchInput.blur();
+        }
+      });
+
+      // ==================== Mobile Menu ====================
+
+      const mobileMenuBtn = document.getElementById('mobile-menu-btn');
+      const mobileMenu = document.getElementById('mobile-menu');
+      const mobileMenuOverlay = document.getElementById('mobile-menu-overlay');
+      const mobileMenuClose = document.getElementById('mobile-menu-close');
+      const mobileSearchLink = document.getElementById('mobile-search-link');
+      const mobileSearchInput = document.getElementById('mobile-search-input');
+      const mobileSearchClear = document.getElementById('mobile-search-clear');
+
+      function openMobileMenu() {
+        mobileMenu.classList.remove('-translate-x-full');
+        mobileMenuOverlay.classList.remove('hidden');
+        document.body.style.overflow = 'hidden';
+      }
+
+      function closeMobileMenu() {
+        mobileMenu.classList.add('-translate-x-full');
+        mobileMenuOverlay.classList.add('hidden');
+        document.body.style.overflow = '';
+      }
+
+      mobileMenuBtn.addEventListener('click', openMobileMenu);
+      mobileMenuClose.addEventListener('click', closeMobileMenu);
+      mobileMenuOverlay.addEventListener('click', closeMobileMenu);
+
+      // Mobile search link - navigate to search results page and focus input
+      mobileSearchLink.addEventListener('click', e => {
+        e.preventDefault();
+        closeMobileMenu();
+
+        // Show search results section
+        document.querySelectorAll('.section').forEach(s => s.classList.add('hidden'));
+        document.getElementById('search-results').classList.remove('hidden');
+        currentSection = 'search-results';
+
+        // Update nav state
+        document.querySelectorAll('.nav-link').forEach(l => {
+          l.classList.remove('bg-primary', 'text-white');
+          l.classList.add('text-slate-800');
+        });
+
+        // Focus mobile search input after a short delay
+        setTimeout(() => mobileSearchInput.focus(), 100);
+      });
+
+      // Close mobile menu when a nav link is clicked
+      document.querySelectorAll('.mobile-nav-link').forEach(link => {
+        link.addEventListener('click', () => {
+          closeMobileMenu();
+          // Also handle section navigation
+          const section = link.dataset.section;
+          if (section) {
+            document.querySelectorAll('.section').forEach(s => s.classList.add('hidden'));
+            document.getElementById(section).classList.remove('hidden');
+            currentSection = section;
+            updateTOC(section);
+
+            // Update desktop nav as well
+            document.querySelectorAll('.nav-link').forEach(l => {
+              l.classList.remove('bg-primary', 'text-white');
+              l.classList.add('text-slate-800');
+              if (l.dataset.section === section) {
+                l.classList.add('bg-primary', 'text-white');
+                l.classList.remove('text-slate-800');
+              }
+            });
+          }
+        });
+      });
+
+      // Mobile search input on search results page
+      mobileSearchInput.addEventListener('input', e => {
+        searchInput.value = e.target.value;
+        debouncedSearch(e.target.value.trim());
+        mobileSearchClear.classList.toggle('hidden', !e.target.value);
+      });
+
+      // Sync desktop search to mobile
+      searchInput.addEventListener('input', e => {
+        mobileSearchInput.value = e.target.value;
+        mobileSearchClear.classList.toggle('hidden', !e.target.value);
+      });
+
+      mobileSearchClear.addEventListener('click', () => {
+        mobileSearchInput.value = '';
+        searchInput.value = '';
+        mobileSearchClear.classList.add('hidden');
+        searchClear.classList.add('hidden');
+        // Clear results but stay on search page with empty state
+        searchResultsContent.innerHTML = '';
+        searchNoResults.classList.add('hidden');
+        searchQueryWrapper.classList.add('hidden');
+        searchEmptyState.classList.remove('hidden');
+        // Update URL to remove search param
+        const url = new URL(window.location);
+        url.searchParams.delete('search');
+        history.replaceState(null, null, url.pathname + url.hash);
+      });
+
+      // Close mobile menu on escape key
+      document.addEventListener('keydown', e => {
+        if (e.key === 'Escape' && !mobileMenu.classList.contains('-translate-x-full')) {
+          closeMobileMenu();
+        }
+      });
+
+      // ==================== Mobile Table of Contents ====================
+
+      const mobileTocLink = document.getElementById('mobile-toc-link');
+      const mobileTocBack = document.getElementById('mobile-toc-back');
+      const mobileMainNav = document.getElementById('mobile-main-nav');
+      const mobileTocNav = document.getElementById('mobile-toc-nav');
+      const mobileTocContent = document.getElementById('mobile-toc-content');
+
+      // Populate mobile ToC based on current section
+      function populateMobileToc() {
+        mobileTocContent.innerHTML = '';
+
+        // Get the current active ToC section from the right sidebar
+        const activeTocSection = document.querySelector('.toc-section:not(.hidden)');
+
+        if (!activeTocSection || activeTocSection.children.length === 0) {
+          // No ToC content for this section
+          mobileTocContent.innerHTML = '<p class="text-slate-500 text-sm px-2">No table of contents available for this section.</p>';
+          return;
+        }
+
+        // Clone the ToC content
+        const clonedContent = activeTocSection.cloneNode(true);
+        clonedContent.classList.remove('hidden', 'toc-section');
+        clonedContent.removeAttribute('id');
+
+        // Update classes for mobile styling
+        clonedContent.querySelectorAll('.toc-link').forEach(link => {
+          link.classList.remove('toc-link');
+          link.classList.add('mobile-toc-link', 'block', 'px-3', 'py-2', 'rounded', 'text-slate-600', 'hover:bg-slate-100', 'hover:text-slate-900', 'transition-colors');
+
+          // Add click handler
+          link.addEventListener('click', e => {
+            e.preventDefault();
+            const href = link.getAttribute('href');
+            const escapedHref = href.replace(/\./g, '\\.');
+            const target = document.querySelector(escapedHref);
+
+            if (target) {
+              closeMobileMenu();
+              setTimeout(() => target.scrollIntoView({ behavior: 'smooth' }), 100);
+              history.pushState(null, null, href);
+            }
+          });
+        });
+
+        // Update group headers for mobile
+        clonedContent.querySelectorAll('.toc-group-header').forEach(header => {
+          header.classList.add('mobile-toc-group-header', 'font-semibold', 'text-sm', 'text-slate-700', 'mb-1', 'px-3', 'py-1');
+        });
+
+        // Update spacing
+        clonedContent.querySelectorAll('ul').forEach(ul => {
+          ul.classList.add('space-y-1', 'text-sm');
+        });
+
+        mobileTocContent.appendChild(clonedContent);
+      }
+
+      // Show mobile ToC
+      function showMobileToc() {
+        populateMobileToc();
+        mobileMainNav.classList.add('hidden');
+        mobileTocNav.classList.remove('hidden');
+      }
+
+      // Show mobile main nav
+      function showMobileMainNav() {
+        mobileTocNav.classList.add('hidden');
+        mobileMainNav.classList.remove('hidden');
+      }
+
+      mobileTocLink.addEventListener('click', showMobileToc);
+      mobileTocBack.addEventListener('click', showMobileMainNav);
+
+      // ==================== Dark Mode Toggle ====================
+
+      const THEME_STORAGE_KEY = 'nf-docs-theme';
+      const themeToggle = document.getElementById('theme-toggle');
+
+      // Get the current theme (from localStorage or system preference)
+      function getCurrentTheme() {
+        const stored = localStorage.getItem(THEME_STORAGE_KEY);
+        if (stored) {
+          return stored;
+        }
+        // Auto-detect from OS preference
+        return window.matchMedia('(prefers-color-scheme: dark)').matches ? 'dark' : 'light';
+      }
+
+      // Apply theme to the document
+      function applyTheme(theme) {
+        if (theme === 'dark') {
+          document.documentElement.classList.add('dark');
+        } else {
+          document.documentElement.classList.remove('dark');
+        }
+      }
+
+      // Toggle theme and save to localStorage
+      function toggleTheme() {
+        const current = getCurrentTheme();
+        const newTheme = current === 'dark' ? 'light' : 'dark';
+        localStorage.setItem(THEME_STORAGE_KEY, newTheme);
+        applyTheme(newTheme);
+      }
+
+      // Theme toggle button click handler
+      themeToggle.addEventListener('click', toggleTheme);
+
+      // Listen for OS theme changes (only if user hasn't set a preference)
+      window.matchMedia('(prefers-color-scheme: dark)').addEventListener('change', e => {
+        const stored = localStorage.getItem(THEME_STORAGE_KEY);
+        if (!stored) {
+          // User hasn't set a preference, follow OS
+          applyTheme(e.matches ? 'dark' : 'light');
+        }
+      });
+
+      // Listen for storage changes from other tabs/windows
+      window.addEventListener('storage', e => {
+        if (e.key === THEME_STORAGE_KEY) {
+          if (e.newValue) {
+            applyTheme(e.newValue);
+          } else {
+            // Storage was cleared, revert to OS preference
+            const osTheme = window.matchMedia('(prefers-color-scheme: dark)').matches ? 'dark' : 'light';
+            applyTheme(osTheme);
+          }
+        }
+      });
+    </script>
+  </body>
+</html>
\ No newline at end of file
diff --git a/docs/examples/nf-fgsv/json/pipeline-api.json b/docs/examples/nf-fgsv/json/pipeline-api.json
new file mode 100644
index 0000000..ed90cb0
--- /dev/null
+++ b/docs/examples/nf-fgsv/json/pipeline-api.json
@@ -0,0 +1,153 @@
+{
+  "pipeline": {
+    "name": "nf-fgsv workflow parameters",
+    "description": "Nextflow workflow for running fgsv.",
+    "version": "0.1.0",
+    "repository": "https://github.com/fulcrumgenomics/nf-fgsv",
+    "authors": [
+      "Fulcrum Genomics"
+    ],
+    "readme_content": "> [!NOTE]  \n> This repository is primarily for testing the latest Nextflow features and the workflow is relatively simple.\n\nThis is a Nextflow workflow for running [fgsv](https://github.com/fulcrumgenomics/fgsv) on a BAM file to gather evidence for structural variation via breakpoint detection.\n\n## Set up Environment\n\nMake sure [Pixi](https://pixi.sh/latest/#installation) and [Docker](https://docs.docker.com/engine/install/) are installed.\n\nThe environment for this analysis is in [pixi.toml](pixi.toml) and is named `nf-fgsv`.\n\nTo install:\n\n```console\npixi install\n```\n\n## Run the Workflow\n\nTo save on typing, a pixi task is available which aliases `nextflow run main.nf`.\n\n```console\npixi run \\\n    nf-workflow \\\n        -profile \"local,docker\" \\\n        --input tests/data/basic_input.tsv\n```\n\n## Available Execution Profiles\n\nSeveral default profiles are available:\n\n* `local` limits the resources used by the workflow to (hopefully) reasonable levels\n* `docker` specifies docker containers should be used for process execution\n* `linux` adds `--user root` to docker `runOptions`\n\n## Inputs\n\nA full description of input parameters is available using the workflow `--help` parameter, `pixi run nf-workflow --help`.\n\nThe required columns in the `--input` samplesheet are:\n\n| Field | Type | Description |\n|-------|------|-------------|\n| `sample` | String, no whitespace | Sample identifier |\n| `bam` | Absolute path | Path to the BAM file for this sample (may be an AWS S3 path) |\n\n### Parameter files\n\nIf using more than a few parameters, consider saving them in a YAML format file (e.g. [tests/integration/params.yml](tests/integration/params.yml)).\n\n```console\npixi run \\\n    nf-workflow \\\n        -profile \"local,docker\" \\\n        -params-file my_params.yml\n```\n\n## Outputs\n\nThe output directory can be specified using the `-output-dir` Nextflow parameter.\nThe default output directory is `results/`.\n`-output-dir` cannot be specified in a `params.yml` file, because it is a Nextflow parameter rather than a workflow parameter.\nIt must be specified on the command line or in a `nextflow.config` file.\n\n```console\npixi run \\\n    nf-workflow \\\n        -profile \"local,docker\" \\\n        --input tests/data/basic_input.tsv \\\n        -output-dir results\n```\n\n<details>\n<summary>Click to toggle output directory structure</summary>\n\n\n```console\nresults\n└── {sample_name}\n    ├── {sample_name}_sorted.bam                # Coordinate-sorted BAM file\n    ├── {sample_name}_svpileup.txt              # SvPileup breakpoint candidates\n    ├── {sample_name}_svpileup.bam              # BAM with SV tags from SvPileup\n    ├── {sample_name}_svpileup.aggregate.txt    # Aggregated/merged breakpoint pileups\n    └── {sample_name}_svpileup.aggregate.bedpe  # Aggregated pileups in BEDPE format\n```\n\n</details>\n\n### Output File Descriptions\n\n| File | Description |\n|------|-------------|\n| `*_sorted.bam` | Input BAM sorted by genomic coordinates using samtools sort |\n| `*_svpileup.txt` | Candidate structural variant breakpoints identified by [fgsv SvPileup](https://github.com/fulcrumgenomics/fgsv) |\n| `*_svpileup.bam` | BAM file with SV-related tags added by SvPileup |\n| `*_svpileup.aggregate.txt` | Merged breakpoint pileups from [fgsv AggregateSvPileup](https://github.com/fulcrumgenomics/fgsv) |\n| `*_svpileup.aggregate.bedpe` | Aggregated pileups converted to [BEDPE format](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format) |\n\n## Contributing\n\nSee our [Contributing Guide](docs/CONTRIBUTING.md) for development and testing guidelines.\n\n\n"
+  },
+  "inputs": [
+    {
+      "name": "input",
+      "type": "string",
+      "description": "Path to tab-separated file containing information about the samples in the experiment.",
+      "required": true,
+      "format": "file-path",
+      "pattern": ".*.tsv$",
+      "group": "Main workflow parameters"
+    }
+  ],
+  "config_params": [],
+  "workflows": [
+    {
+      "name": "",
+      "docstring": "",
+      "file": "main.nf",
+      "line": 19,
+      "end_line": 42,
+      "inputs": [],
+      "outputs": [],
+      "calls": [],
+      "is_entry": true,
+      "source_url": "https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/main.nf#L19-L42"
+    }
+  ],
+  "processes": [
+    {
+      "name": "AGGREGATE_SV_PILEUP_TO_BEDPE",
+      "docstring": "Convert aggregated SvPileup output to BEDPE format using fgsv\nAggregateSvPileupToBedPE.",
+      "file": "modules/aggregate_sv_pileup_to_bedpe.nf",
+      "line": 11,
+      "end_line": 31,
+      "inputs": [
+        {
+          "name": "val(meta), path(txt)",
+          "type": "tuple",
+          "description": "`meta`: Map containing sample information (must include 'id'); `txt`: Aggregated SvPileup output file",
+          "qualifier": "Tuple<Map, Path>"
+        }
+      ],
+      "outputs": [
+        {
+          "name": "val(meta), file(\"*_svpileup.aggregate.bedpe\")",
+          "type": "tuple",
+          "description": "Tuple of meta and BEDPE format output file",
+          "emit": "bedpe"
+        }
+      ],
+      "directives": {},
+      "source_url": "https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/aggregate_sv_pileup_to_bedpe.nf#L11-L31"
+    },
+    {
+      "name": "AGGREGATE_SV_PILEUP",
+      "docstring": "Aggregate and merge pileups that are likely to support the same breakpoint\nusing fgsv AggregateSvPileup.",
+      "file": "modules/aggregate_sv_pileup.nf",
+      "line": 12,
+      "end_line": 33,
+      "inputs": [
+        {
+          "name": "val(meta), path(bam), path(txt)",
+          "type": "tuple",
+          "description": "`meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file; `txt`: SvPileup breakpoint output file",
+          "qualifier": "Tuple<Map, Path, Path>"
+        }
+      ],
+      "outputs": [
+        {
+          "name": "val(meta), file(\"*_svpileup.aggregate.txt\")",
+          "type": "tuple",
+          "description": "Tuple of meta and aggregated SvPileup output file",
+          "emit": "txt"
+        }
+      ],
+      "directives": {},
+      "source_url": "https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/aggregate_sv_pileup.nf#L12-L33"
+    },
+    {
+      "name": "COORDINATE_SORT",
+      "docstring": "Sort a BAM file by genomic coordinates using samtools sort.",
+      "file": "modules/coordinate_sort.nf",
+      "line": 10,
+      "end_line": 31,
+      "inputs": [
+        {
+          "name": "val(meta), path(bam)",
+          "type": "tuple",
+          "description": "`meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file to be sorted",
+          "qualifier": "Tuple<Map, Path>"
+        }
+      ],
+      "outputs": [
+        {
+          "name": "val(meta), file(\"*_sorted.bam\")",
+          "type": "tuple",
+          "description": "Tuple of meta and coordinate-sorted BAM file",
+          "emit": "bam"
+        }
+      ],
+      "directives": {},
+      "source_url": "https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/coordinate_sort.nf#L10-L31"
+    },
+    {
+      "name": "SV_PILEUP",
+      "docstring": "Detect structural variant evidence from a BAM file using fgsv SvPileup.",
+      "file": "modules/sv_pileup.nf",
+      "line": 11,
+      "end_line": 33,
+      "inputs": [
+        {
+          "name": "val(meta), path(bam)",
+          "type": "tuple",
+          "description": "`meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file",
+          "qualifier": "Tuple<Map, Path>"
+        }
+      ],
+      "outputs": [
+        {
+          "name": "val(meta), file(\"*_svpileup.txt\")",
+          "type": "tuple",
+          "description": "Tuple of meta and SvPileup breakpoint output file",
+          "emit": "txt"
+        },
+        {
+          "name": "val(meta), file(\"*_svpileup.bam\")",
+          "type": "tuple",
+          "description": "Tuple of meta and SvPileup BAM file",
+          "emit": "bam"
+        }
+      ],
+      "directives": {},
+      "source_url": "https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/sv_pileup.nf#L11-L33"
+    }
+  ],
+  "functions": [],
+  "generated_by": {
+    "nf_docs_version": "0.2.0",
+    "generated_at": "2026-03-03T19:13:49.416189+00:00",
+    "nextflow_url": "https://nextflow.io",
+    "nf_docs_url": "https://github.com/ewels/nf-docs"
+  }
+}
\ No newline at end of file
diff --git a/docs/examples/nf-fgsv/markdown/index.md b/docs/examples/nf-fgsv/markdown/index.md
new file mode 100644
index 0000000..88cd9cf
--- /dev/null
+++ b/docs/examples/nf-fgsv/markdown/index.md
@@ -0,0 +1,30 @@
+# nf-fgsv workflow parameters
+
+**Version:** 0.1.0
+
+Nextflow workflow for running fgsv.
+
+## Documentation
+
+- [Pipeline Inputs](inputs.md) - Input parameters and options
+- [Workflows](workflows.md) - Pipeline workflows
+- [Processes](processes.md) - Process definitions
+
+## Summary
+
+- **Inputs:** 1 parameters
+- **Workflows:** 1
+- **Processes:** 4
+
+## Authors
+
+- Fulcrum Genomics
+
+## Links
+
+- [Repository](https://github.com/fulcrumgenomics/nf-fgsv)
+
+---
+
+*This pipeline was built with [Nextflow](https://nextflow.io).
+Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 19:14:06 UTC.*
diff --git a/docs/examples/nf-fgsv/markdown/inputs.md b/docs/examples/nf-fgsv/markdown/inputs.md
new file mode 100644
index 0000000..c3bb522
--- /dev/null
+++ b/docs/examples/nf-fgsv/markdown/inputs.md
@@ -0,0 +1,20 @@
+# Pipeline Inputs
+
+This page documents all input parameters for the pipeline.
+
+## Main workflow parameters
+
+### `--input` {#input}
+
+**Type:** `string` | **Required** | **Format:** `file-path`
+
+Path to tab-separated file containing information about the samples in the experiment.
+
+**Pattern:** `.*.tsv$`
+
+
+
+---
+
+*This pipeline was built with [Nextflow](https://nextflow.io).
+Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 19:14:06 UTC.*
diff --git a/docs/examples/nf-fgsv/markdown/processes.md b/docs/examples/nf-fgsv/markdown/processes.md
new file mode 100644
index 0000000..693201f
--- /dev/null
+++ b/docs/examples/nf-fgsv/markdown/processes.md
@@ -0,0 +1,94 @@
+# Processes
+
+This page documents all processes in the pipeline.
+
+## Contents
+
+- [AGGREGATE_SV_PILEUP_TO_BEDPE](#aggregate-sv-pileup-to-bedpe)
+- [AGGREGATE_SV_PILEUP](#aggregate-sv-pileup)
+- [COORDINATE_SORT](#coordinate-sort)
+- [SV_PILEUP](#sv-pileup)
+
+## AGGREGATE_SV_PILEUP_TO_BEDPE {#aggregate-sv-pileup-to-bedpe}
+
+*Defined in `modules/aggregate_sv_pileup_to_bedpe.nf:11`*
+
+Convert aggregated SvPileup output to BEDPE format using fgsv
+AggregateSvPileupToBedPE.
+
+### Inputs
+
+| Name | Type | Description |
+|------|------|-------------|
+| `val(meta), path(txt)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `txt`: Aggregated SvPileup output file |
+
+### Outputs
+
+| Name | Type | Emit | Description |
+|------|------|------|-------------|
+| `val(meta), file("*_svpileup.aggregate.bedpe")` | `tuple` | `bedpe` | Tuple of meta and BEDPE format output file |
+
+
+## AGGREGATE_SV_PILEUP {#aggregate-sv-pileup}
+
+*Defined in `modules/aggregate_sv_pileup.nf:12`*
+
+Aggregate and merge pileups that are likely to support the same breakpoint
+using fgsv AggregateSvPileup.
+
+### Inputs
+
+| Name | Type | Description |
+|------|------|-------------|
+| `val(meta), path(bam), path(txt)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file; `txt`: SvPileup breakpoint output file |
+
+### Outputs
+
+| Name | Type | Emit | Description |
+|------|------|------|-------------|
+| `val(meta), file("*_svpileup.aggregate.txt")` | `tuple` | `txt` | Tuple of meta and aggregated SvPileup output file |
+
+
+## COORDINATE_SORT {#coordinate-sort}
+
+*Defined in `modules/coordinate_sort.nf:10`*
+
+Sort a BAM file by genomic coordinates using samtools sort.
+
+### Inputs
+
+| Name | Type | Description |
+|------|------|-------------|
+| `val(meta), path(bam)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file to be sorted |
+
+### Outputs
+
+| Name | Type | Emit | Description |
+|------|------|------|-------------|
+| `val(meta), file("*_sorted.bam")` | `tuple` | `bam` | Tuple of meta and coordinate-sorted BAM file |
+
+
+## SV_PILEUP {#sv-pileup}
+
+*Defined in `modules/sv_pileup.nf:11`*
+
+Detect structural variant evidence from a BAM file using fgsv SvPileup.
+
+### Inputs
+
+| Name | Type | Description |
+|------|------|-------------|
+| `val(meta), path(bam)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file |
+
+### Outputs
+
+| Name | Type | Emit | Description |
+|------|------|------|-------------|
+| `val(meta), file("*_svpileup.txt")` | `tuple` | `txt` | Tuple of meta and SvPileup breakpoint output file |
+| `val(meta), file("*_svpileup.bam")` | `tuple` | `bam` | Tuple of meta and SvPileup BAM file |
+
+
+---
+
+*This pipeline was built with [Nextflow](https://nextflow.io).
+Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 19:14:06 UTC.*
diff --git a/docs/examples/nf-fgsv/markdown/workflows.md b/docs/examples/nf-fgsv/markdown/workflows.md
new file mode 100644
index 0000000..a14b179
--- /dev/null
+++ b/docs/examples/nf-fgsv/markdown/workflows.md
@@ -0,0 +1,19 @@
+# Workflows
+
+This page documents all workflows in the pipeline.
+
+## Contents
+
+- [(entry)](#entry) *(entry point)*
+
+## (entry) {#entry}
+
+**Entry workflow**
+
+*Defined in `main.nf:19`*
+
+
+---
+
+*This pipeline was built with [Nextflow](https://nextflow.io).
+Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 19:14:06 UTC.*

From 3bdae14d35168cf5332d167bb6b7a135ba87154f Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Tue, 3 Mar 2026 23:04:17 +0100
Subject: [PATCH 8/9] Refactor: eliminate duplicated file reads and extract
 shared constants

Read .nf source files once per process instead of twice (once for
Groovydoc parsing, once for output enrichment). Extract duplicated
section-boundary regexes and _return_ key prefix strings as shared
constants to keep parsers in sync.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 src/nf_docs/extractor.py  | 53 +++++++++++++++++++++++----------------
 src/nf_docs/lsp_client.py |  7 +++---
 src/nf_docs/nf_parser.py  | 49 +++++++++++++++++-------------------
 tests/test_extractor.py   | 24 +++++-------------
 tests/test_nf_parser.py   | 45 ++++++++++-----------------------
 5 files changed, 77 insertions(+), 101 deletions(-)

diff --git a/src/nf_docs/extractor.py b/src/nf_docs/extractor.py
index 4fdf601..e4224df 100644
--- a/src/nf_docs/extractor.py
+++ b/src/nf_docs/extractor.py
@@ -38,7 +38,13 @@
     WorkflowInput,
     WorkflowOutput,
 )
-from nf_docs.nf_parser import enrich_outputs_from_source, parse_process_hover, parse_workflow_hover
+from nf_docs.nf_parser import (
+    RETURN_KEY_PREFIX,
+    RETURN_KEY_UNNAMED,
+    enrich_outputs_from_source,
+    parse_process_hover,
+    parse_workflow_hover,
+)
 from nf_docs.progress import (
     ExtractionPhase,
     ProgressCallbackType,
@@ -659,11 +665,19 @@ def _create_process_from_signature(
         if param_docs is None:
             param_docs = {}
 
+        # Read the source file once — shared by Groovydoc parsing and output enrichment.
+        source_text: str | None = None
+        if source_path:
+            try:
+                source_text = source_path.read_text(encoding="utf-8")
+            except OSError as e:
+                logger.debug(f"Could not read source file {source_path}: {e}")
+
         # If the LSP returned no param docs, try to parse them from the source file.
         # The LSP may return the free-text docstring but strip @param/@return tags,
         # or (for typed processes) return no docstring at all.
-        if source_path and not param_docs:
-            source_docstring, source_params = _parse_groovydoc_from_source(source_path, name)
+        if source_text is not None and not param_docs:
+            source_docstring, source_params = _parse_groovydoc_from_source(source_text, name)
             if source_params:
                 param_docs = source_params
             if not docstring and source_docstring:
@@ -684,8 +698,8 @@ def _create_process_from_signature(
             # Enrich bare-name outputs from the source file when the LSP
             # only returns emit names (common with typed Nextflow syntax)
             outputs = parsed.outputs
-            if source_path and any(not o.type for o in outputs):
-                outputs = enrich_outputs_from_source(outputs, source_path, name)
+            if source_text is not None and any(not o.type for o in outputs):
+                outputs = enrich_outputs_from_source(outputs, source_text, name)
 
             for inp in parsed.inputs:
                 # Look up @param description by matching input component names
@@ -700,9 +714,9 @@ def _create_process_from_signature(
                 )
             for out in outputs:
                 # Look up @return description by emit name
-                description = param_docs.get(f"_return_{out.emit}", "")
+                description = param_docs.get(f"{RETURN_KEY_PREFIX}{out.emit}", "")
                 if not description:
-                    description = param_docs.get("_return", "")
+                    description = param_docs.get(RETURN_KEY_UNNAMED, "")
                 process.outputs.append(
                     ProcessOutput(
                         name=out.name,
@@ -773,7 +787,7 @@ def _create_function_from_signature(
             line=line,
             end_line=end_line,
             source_url=source_url,
-            return_description=param_docs.get("_return", ""),
+            return_description=param_docs.get(RETURN_KEY_UNNAMED, ""),
         )
 
         # Parse function signature: def name(param1: Type, param2: Type) -> ReturnType
@@ -842,14 +856,14 @@ def _find_param_description(input_name: str, param_docs: dict[str, str]) -> str:
 
 
 def _parse_groovydoc_from_source(
-    source_path: Path,
+    source: str,
     process_name: str,
 ) -> tuple[str, dict[str, str]]:
-    """Parse a Groovydoc comment from a ``.nf`` source file.
+    """Parse a Groovydoc comment from ``.nf`` source text.
 
     When the Nextflow LSP does not return a docstring (common with typed
-    processes), this function reads the source file and extracts the
-    ``/** ... */`` comment block preceding the process definition.
+    processes), this function extracts the ``/** ... */`` comment block
+    preceding the process definition.
 
     Supports two documentation styles:
 
@@ -869,7 +883,7 @@ def _parse_groovydoc_from_source(
          */
 
     Args:
-        source_path: Absolute path to the ``.nf`` source file.
+        source: The ``.nf`` source file contents.
         process_name: Name of the process to locate.
 
     Returns:
@@ -877,11 +891,6 @@ def _parse_groovydoc_from_source(
         description and *param_docs* maps param/return names to descriptions.
         Returns ``("", {})`` if no Groovydoc is found.
     """
-    try:
-        source = source_path.read_text(encoding="utf-8")
-    except OSError as e:
-        logger.debug(f"Could not read source file {source_path} for Groovydoc: {e}")
-        return "", {}
 
     # Find the process declaration, then look backwards for the nearest /** ... */
     proc_pattern = re.compile(
@@ -945,7 +954,7 @@ def _parse_groovydoc_comment(comment_body: str) -> tuple[str, dict[str, str]]:
         return_named = re.match(r"@returns?\s+(\w+)\s+(.*)", line)
         if return_named:
             current_section = "return"
-            current_param = f"_return_{return_named.group(1)}"
+            current_param = f"{RETURN_KEY_PREFIX}{return_named.group(1)}"
             params[current_param] = return_named.group(2).strip()
             continue
 
@@ -953,8 +962,8 @@ def _parse_groovydoc_comment(comment_body: str) -> tuple[str, dict[str, str]]:
         return_unnamed = re.match(r"@returns?\s*(.*)", line)
         if return_unnamed:
             current_section = "return"
-            current_param = "_return"
-            params["_return"] = return_unnamed.group(1).strip()
+            current_param = RETURN_KEY_UNNAMED
+            params[RETURN_KEY_UNNAMED] = return_unnamed.group(1).strip()
             continue
 
         # --- Bullet-list Inputs: / Outputs: sections ---
@@ -976,7 +985,7 @@ def _parse_groovydoc_comment(comment_body: str) -> tuple[str, dict[str, str]]:
                 current_param = name
                 params[name] = desc
             else:
-                current_param = f"_return_{name}"
+                current_param = f"{RETURN_KEY_PREFIX}{name}"
                 params[current_param] = desc
             continue
 
diff --git a/src/nf_docs/lsp_client.py b/src/nf_docs/lsp_client.py
index f6e0e74..618afca 100644
--- a/src/nf_docs/lsp_client.py
+++ b/src/nf_docs/lsp_client.py
@@ -24,6 +24,7 @@
 import httpx
 
 from nf_docs.nextflow_env import get_isolated_env
+from nf_docs.nf_parser import RETURN_KEY_PREFIX, RETURN_KEY_UNNAMED
 from nf_docs.progress import (
     ExtractionPhase,
     ProgressCallbackType,
@@ -878,14 +879,14 @@ def parse_hover_content(hover: dict[str, Any] | None) -> tuple[str, str, dict[st
             return_match = re.match(r"@returns?\s+(\w+)\s+(.*)", line_stripped)
             if return_match:
                 current_section = "return"
-                current_param = f"_return_{return_match.group(1)}"
+                current_param = f"{RETURN_KEY_PREFIX}{return_match.group(1)}"
                 params[current_param] = return_match.group(2).strip()
                 continue
             return_unnamed = re.match(r"@returns?\s*(.*)", line_stripped)
             if return_unnamed:
                 current_section = "return"
-                current_param = "_return"
-                params["_return"] = return_unnamed.group(1).strip()
+                current_param = RETURN_KEY_UNNAMED
+                params[RETURN_KEY_UNNAMED] = return_unnamed.group(1).strip()
                 continue
 
             # Handle continuation lines
diff --git a/src/nf_docs/nf_parser.py b/src/nf_docs/nf_parser.py
index 27bd5d1..a91ebb8 100644
--- a/src/nf_docs/nf_parser.py
+++ b/src/nf_docs/nf_parser.py
@@ -8,12 +8,24 @@
 import logging
 import re
 from dataclasses import dataclass, field
-from pathlib import Path
 
 # Traditional Nextflow input qualifiers that should not be treated as typed variable names.
 # Used to prevent false matches like "each: sample" being parsed as typed input "each" of type "sample".
 _TRADITIONAL_QUALIFIERS = frozenset({"val", "path", "file", "env", "stdin", "tuple", "each"})
 
+# Key prefix used in param_docs dicts to distinguish @return entries from @param entries.
+RETURN_KEY_PREFIX = "_return_"
+RETURN_KEY_UNNAMED = "_return"
+
+# Regexes for extracting input/output sections from a process body.
+# The terminators cover every Nextflow process section keyword.
+_INPUT_SECTION_RE = re.compile(
+    r"input:\s*(.*?)(?:output:|topic:|script:|shell:|exec:|\})", re.DOTALL
+)
+_OUTPUT_SECTION_RE = re.compile(
+    r"output:\s*(.*?)(?:topic:|script:|shell:|exec:|when:|\})", re.DOTALL
+)
+
 logger = logging.getLogger(__name__)
 
 
@@ -92,17 +104,13 @@ def parse_process_hover(hover_text: str) -> ParsedProcess | None:
     process = ParsedProcess(name=name_match.group(1))
 
     # Extract input section
-    input_match = re.search(
-        r"input:\s*(.*?)(?:output:|topic:|script:|shell:|exec:|\})", code, re.DOTALL
-    )
+    input_match = _INPUT_SECTION_RE.search(code)
     if input_match:
         input_block = input_match.group(1)
         process.inputs = _parse_input_declarations(input_block)
 
     # Extract output section
-    output_match = re.search(
-        r"output:\s*(.*?)(?:topic:|script:|shell:|exec:|when:|\})", code, re.DOTALL
-    )
+    output_match = _OUTPUT_SECTION_RE.search(code)
     if output_match:
         output_block = output_match.group(1)
         process.outputs = _parse_output_declarations(output_block)
@@ -458,15 +466,15 @@ def is_code_block(text: str) -> bool:
 
 def enrich_outputs_from_source(
     outputs: list[ParsedOutput],
-    source_path: Path,
+    source: str,
     process_name: str,
 ) -> list[ParsedOutput]:
-    """Enrich bare-name outputs with full declarations parsed from the ``.nf`` source.
+    """Enrich bare-name outputs with full declarations parsed from ``.nf`` source text.
 
     When the Nextflow LSP returns bare emit names for typed process outputs
     (e.g. ``txt``, ``bam`` instead of ``txt = tuple(meta, file("*.txt"))``),
-    this function reads the actual source file and parses the named-assignment
-    output declarations to provide full type and component information.
+    this function parses the source text to find the named-assignment
+    output declarations and provide full type and component information.
 
     If a bare output's emit name matches a named assignment in the source, the
     bare output is replaced with the richer parsed version.  Outputs that are
@@ -474,28 +482,21 @@ def enrich_outputs_from_source(
 
     Args:
         outputs: The outputs parsed from the LSP hover (may contain bare names).
-        source_path: Absolute path to the ``.nf`` source file.
+        source: The ``.nf`` source file contents.
         process_name: Name of the process to locate in the source.
 
     Returns:
         A new list of ``ParsedOutput`` objects, enriched where possible.
     """
     # Only enrich if there are bare outputs (type is empty)
-    bare_outputs = [o for o in outputs if not o.type]
-    if not bare_outputs:
-        return outputs
-
-    try:
-        source = source_path.read_text(encoding="utf-8")
-    except OSError as e:
-        logger.debug(f"Could not read source file {source_path} for output enrichment: {e}")
+    if not any(not o.type for o in outputs):
         return outputs
 
     # Find the process block in source
     proc_pattern = re.compile(rf"process\s+{re.escape(process_name)}\s*\{{", re.MULTILINE)
     proc_match = proc_pattern.search(source)
     if not proc_match:
-        logger.debug(f"Could not find process {process_name} in {source_path}")
+        logger.debug(f"Could not find process {process_name} in source")
         return outputs
 
     # Extract the process body (find matching closing brace)
@@ -515,11 +516,7 @@ def enrich_outputs_from_source(
         return outputs
 
     # Extract the output section from the source process body
-    output_match = re.search(
-        r"output:\s*(.*?)(?:topic:|script:|shell:|exec:|when:|\})",
-        proc_body,
-        re.DOTALL,
-    )
+    output_match = _OUTPUT_SECTION_RE.search(proc_body)
     if not output_match:
         return outputs
 
diff --git a/tests/test_extractor.py b/tests/test_extractor.py
index 321d31c..535b1d8 100644
--- a/tests/test_extractor.py
+++ b/tests/test_extractor.py
@@ -204,7 +204,7 @@ def test_parse_groovydoc_bullet_format(self):
         assert params["bam"] == "Input BAM file"
         assert params["_return_txt"] == "SvPileup breakpoint output"
 
-    def test_parse_groovydoc_from_source_with_intervening_code(self, tmp_path: Path):
+    def test_parse_groovydoc_from_source_with_intervening_code(self):
         """Groovydoc with code between */ and process declaration."""
         from nf_docs.extractor import _parse_groovydoc_from_source
 
@@ -226,31 +226,19 @@ def test_parse_groovydoc_from_source_with_intervening_code(self, tmp_path: Path)
     bam
 }
 """
-        nf_file = tmp_path / "sv_pileup.nf"
-        nf_file.write_text(source)
-
-        docstring, params = _parse_groovydoc_from_source(nf_file, "SV_PILEUP")
+        docstring, params = _parse_groovydoc_from_source(source, "SV_PILEUP")
         assert "Detect SVs from BAM" in docstring
         assert params["meta"] == "Sample metadata"
         assert params["bam"] == "Input BAM"
         assert params["_return_txt"] == "Output text file"
 
-    def test_parse_groovydoc_from_source_not_found(self, tmp_path: Path):
+    def test_parse_groovydoc_from_source_not_found(self):
         """Returns empty when process not found in source."""
         from nf_docs.extractor import _parse_groovydoc_from_source
 
-        nf_file = tmp_path / "other.nf"
-        nf_file.write_text("process OTHER { script: '' }\n")
-
-        docstring, params = _parse_groovydoc_from_source(nf_file, "MISSING")
-        assert docstring == ""
-        assert params == {}
-
-    def test_parse_groovydoc_from_source_no_file(self, tmp_path: Path):
-        """Returns empty when source file doesn't exist."""
-        from nf_docs.extractor import _parse_groovydoc_from_source
-
-        docstring, params = _parse_groovydoc_from_source(tmp_path / "nonexistent.nf", "PROC")
+        docstring, params = _parse_groovydoc_from_source(
+            "process OTHER { script: '' }\n", "MISSING"
+        )
         assert docstring == ""
         assert params == {}
 
diff --git a/tests/test_nf_parser.py b/tests/test_nf_parser.py
index 9316477..f02d47e 100644
--- a/tests/test_nf_parser.py
+++ b/tests/test_nf_parser.py
@@ -1,7 +1,5 @@
 """Tests for the Nextflow code parser."""
 
-from pathlib import Path
-
 from nf_docs.nf_parser import (
     ParsedInput,
     ParsedOutput,
@@ -585,16 +583,13 @@ def prefix = "${meta.id}"
 }
 """
 
-    def test_bare_outputs_enriched(self, tmp_path: Path):
+    def test_bare_outputs_enriched(self):
         """Bare emit names are replaced with full declarations from source."""
-        source_file = tmp_path / "sv_pileup.nf"
-        source_file.write_text(self.SV_PILEUP_SOURCE)
-
         bare_outputs = [
             ParsedOutput(name="txt", type="", emit="txt"),
             ParsedOutput(name="bam", type="", emit="bam"),
         ]
-        result = enrich_outputs_from_source(bare_outputs, source_file, "SV_PILEUP")
+        result = enrich_outputs_from_source(bare_outputs, self.SV_PILEUP_SOURCE, "SV_PILEUP")
 
         assert len(result) == 2
         assert result[0].emit == "txt"
@@ -604,59 +599,45 @@ def test_bare_outputs_enriched(self, tmp_path: Path):
         assert result[1].type == "tuple"
         assert "file(" in result[1].name
 
-    def test_already_qualified_outputs_not_changed(self, tmp_path: Path):
+    def test_already_qualified_outputs_not_changed(self):
         """Outputs that already have a type are left untouched."""
-        source_file = tmp_path / "sv_pileup.nf"
-        source_file.write_text(self.SV_PILEUP_SOURCE)
-
         qualified_outputs = [
             ParsedOutput(name="val(meta), path(*.html)", type="tuple", emit="html"),
         ]
-        result = enrich_outputs_from_source(qualified_outputs, source_file, "SV_PILEUP")
+        result = enrich_outputs_from_source(qualified_outputs, self.SV_PILEUP_SOURCE, "SV_PILEUP")
 
         assert len(result) == 1
         assert result[0] is qualified_outputs[0]  # same object, unchanged
 
-    def test_missing_source_file_returns_originals(self, tmp_path: Path):
-        """If the source file doesn't exist, return outputs unchanged."""
-        bare_outputs = [ParsedOutput(name="txt", type="", emit="txt")]
-        result = enrich_outputs_from_source(bare_outputs, tmp_path / "nonexistent.nf", "SV_PILEUP")
-        assert result is bare_outputs
-
-    def test_process_not_found_returns_originals(self, tmp_path: Path):
+    def test_process_not_found_returns_originals(self):
         """If the process name isn't in the source, return outputs unchanged."""
-        source_file = tmp_path / "other.nf"
-        source_file.write_text("process OTHER_PROC {\n  output:\n  x = val(1)\n}\n")
-
         bare_outputs = [ParsedOutput(name="txt", type="", emit="txt")]
-        result = enrich_outputs_from_source(bare_outputs, source_file, "SV_PILEUP")
+        result = enrich_outputs_from_source(
+            bare_outputs, "process OTHER_PROC {\n  output:\n  x = val(1)\n}\n", "SV_PILEUP"
+        )
         assert result is bare_outputs
 
-    def test_partial_match_enriches_only_matching(self, tmp_path: Path):
+    def test_partial_match_enriches_only_matching(self):
         """Only bare outputs whose emit matches a source declaration are enriched."""
-        source_file = tmp_path / "sv_pileup.nf"
-        source_file.write_text(self.SV_PILEUP_SOURCE)
-
         outputs = [
             ParsedOutput(name="txt", type="", emit="txt"),
             ParsedOutput(name="unknown", type="", emit="unknown"),
         ]
-        result = enrich_outputs_from_source(outputs, source_file, "SV_PILEUP")
+        result = enrich_outputs_from_source(outputs, self.SV_PILEUP_SOURCE, "SV_PILEUP")
 
         assert result[0].type == "tuple"  # enriched
         assert result[0].emit == "txt"
         assert result[1].type == ""  # not found in source, unchanged
         assert result[1].emit == "unknown"
 
-    def test_simple_named_output(self, tmp_path: Path):
+    def test_simple_named_output(self):
         """Named simple output: versions = path("versions.yml")."""
-        source_file = tmp_path / "proc.nf"
-        source_file.write_text(
+        source = (
             'process SIMPLE {\n  output:\n  versions = path("versions.yml")\n\n  script:\n  ""\n}\n'
         )
 
         bare_outputs = [ParsedOutput(name="versions", type="", emit="versions")]
-        result = enrich_outputs_from_source(bare_outputs, source_file, "SIMPLE")
+        result = enrich_outputs_from_source(bare_outputs, source, "SIMPLE")
 
         assert result[0].emit == "versions"
         assert result[0].type == "path"

From 91a8e9954085cdbbc99fc2577b1da75482e95791 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Tue, 3 Mar 2026 23:50:38 +0100
Subject: [PATCH 9/9] Add YAML and Table example outputs for nf-fgsv

---
 docs/examples/nf-fgsv/table/README.md        |  83 +++++++++++
 docs/examples/nf-fgsv/yaml/pipeline-api.yaml | 144 +++++++++++++++++++
 2 files changed, 227 insertions(+)
 create mode 100644 docs/examples/nf-fgsv/table/README.md
 create mode 100644 docs/examples/nf-fgsv/yaml/pipeline-api.yaml

diff --git a/docs/examples/nf-fgsv/table/README.md b/docs/examples/nf-fgsv/table/README.md
new file mode 100644
index 0000000..ab74682
--- /dev/null
+++ b/docs/examples/nf-fgsv/table/README.md
@@ -0,0 +1,83 @@
+<!-- BEGIN_NF_DOCS -->
+# nf-fgsv workflow parameters
+
+**Version:** 0.1.0 · Nextflow workflow for running fgsv.
+
+## Inputs
+
+### Main workflow parameters
+
+| Name | Description | Type | Default | Required |
+|------|-------------|------|---------|:--------:|
+| `--input` | Path to tab-separated file containing information about the samples in the experiment. | `string` | n/a | yes |
+
+## Workflows
+
+| Name | Description | Entry |
+|------|-------------|:-----:|
+| *(entry)* | n/a | yes |
+
+## Processes
+
+| Name | Description |
+|------|-------------|
+| `AGGREGATE_SV_PILEUP_TO_BEDPE` | Convert aggregated SvPileup output to BEDPE format using fgsv AggregateSvPileupToBedPE. |
+| `AGGREGATE_SV_PILEUP` | Aggregate and merge pileups that are likely to support the same breakpoint using fgsv AggregateSvPileup. |
+| `COORDINATE_SORT` | Sort a BAM file by genomic coordinates using samtools sort. |
+| `SV_PILEUP` | Detect structural variant evidence from a BAM file using fgsv SvPileup. |
+
+### `AGGREGATE_SV_PILEUP_TO_BEDPE` Inputs
+
+| Name | Type | Description |
+|------|------|-------------|
+| `val(meta), path(txt)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `txt`: Aggregated SvPileup output file |
+
+### `AGGREGATE_SV_PILEUP_TO_BEDPE` Outputs
+
+| Name | Type | Emit | Description |
+|------|------|------|-------------|
+| `val(meta), file("*_svpileup.aggregate.bedpe")` | `tuple` | `bedpe` | Tuple of meta and BEDPE format output file |
+
+### `AGGREGATE_SV_PILEUP` Inputs
+
+| Name | Type | Description |
+|------|------|-------------|
+| `val(meta), path(bam), path(txt)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file; `txt`: SvPileup breakpoint output file |
+
+### `AGGREGATE_SV_PILEUP` Outputs
+
+| Name | Type | Emit | Description |
+|------|------|------|-------------|
+| `val(meta), file("*_svpileup.aggregate.txt")` | `tuple` | `txt` | Tuple of meta and aggregated SvPileup output file |
+
+### `COORDINATE_SORT` Inputs
+
+| Name | Type | Description |
+|------|------|-------------|
+| `val(meta), path(bam)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file to be sorted |
+
+### `COORDINATE_SORT` Outputs
+
+| Name | Type | Emit | Description |
+|------|------|------|-------------|
+| `val(meta), file("*_sorted.bam")` | `tuple` | `bam` | Tuple of meta and coordinate-sorted BAM file |
+
+### `SV_PILEUP` Inputs
+
+| Name | Type | Description |
+|------|------|-------------|
+| `val(meta), path(bam)` | `tuple` | `meta`: Map containing sample information (must include 'id'); `bam`: Input BAM file |
+
+### `SV_PILEUP` Outputs
+
+| Name | Type | Emit | Description |
+|------|------|------|-------------|
+| `val(meta), file("*_svpileup.txt")` | `tuple` | `txt` | Tuple of meta and SvPileup breakpoint output file |
+| `val(meta), file("*_svpileup.bam")` | `tuple` | `bam` | Tuple of meta and SvPileup BAM file |
+
+---
+
+*This pipeline was built with [Nextflow](https://nextflow.io).
+Documentation generated by [nf-docs](https://github.com/ewels/nf-docs) v0.2.0 on 2026-03-03 22:49:08 UTC.*
+
+<!-- END_NF_DOCS -->
diff --git a/docs/examples/nf-fgsv/yaml/pipeline-api.yaml b/docs/examples/nf-fgsv/yaml/pipeline-api.yaml
new file mode 100644
index 0000000..b7a24db
--- /dev/null
+++ b/docs/examples/nf-fgsv/yaml/pipeline-api.yaml
@@ -0,0 +1,144 @@
+pipeline:
+  name: nf-fgsv workflow parameters
+  description: Nextflow workflow for running fgsv.
+  version: 0.1.0
+  repository: https://github.com/fulcrumgenomics/nf-fgsv
+  authors:
+  - Fulcrum Genomics
+  readme_content: "> [!NOTE]  \n> This repository is primarily for testing the latest Nextflow features\
+    \ and the workflow is relatively simple.\n\nThis is a Nextflow workflow for running [fgsv](https://github.com/fulcrumgenomics/fgsv)\
+    \ on a BAM file to gather evidence for structural variation via breakpoint detection.\n\n## Set up\
+    \ Environment\n\nMake sure [Pixi](https://pixi.sh/latest/#installation) and [Docker](https://docs.docker.com/engine/install/)\
+    \ are installed.\n\nThe environment for this analysis is in [pixi.toml](pixi.toml) and is named `nf-fgsv`.\n\
+    \nTo install:\n\n```console\npixi install\n```\n\n## Run the Workflow\n\nTo save on typing, a pixi\
+    \ task is available which aliases `nextflow run main.nf`.\n\n```console\npixi run \\\n    nf-workflow\
+    \ \\\n        -profile \"local,docker\" \\\n        --input tests/data/basic_input.tsv\n```\n\n##\
+    \ Available Execution Profiles\n\nSeveral default profiles are available:\n\n* `local` limits the\
+    \ resources used by the workflow to (hopefully) reasonable levels\n* `docker` specifies docker containers\
+    \ should be used for process execution\n* `linux` adds `--user root` to docker `runOptions`\n\n##\
+    \ Inputs\n\nA full description of input parameters is available using the workflow `--help` parameter,\
+    \ `pixi run nf-workflow --help`.\n\nThe required columns in the `--input` samplesheet are:\n\n| Field\
+    \ | Type | Description |\n|-------|------|-------------|\n| `sample` | String, no whitespace | Sample\
+    \ identifier |\n| `bam` | Absolute path | Path to the BAM file for this sample (may be an AWS S3 path)\
+    \ |\n\n### Parameter files\n\nIf using more than a few parameters, consider saving them in a YAML\
+    \ format file (e.g. [tests/integration/params.yml](tests/integration/params.yml)).\n\n```console\n\
+    pixi run \\\n    nf-workflow \\\n        -profile \"local,docker\" \\\n        -params-file my_params.yml\n\
+    ```\n\n## Outputs\n\nThe output directory can be specified using the `-output-dir` Nextflow parameter.\n\
+    The default output directory is `results/`.\n`-output-dir` cannot be specified in a `params.yml` file,\
+    \ because it is a Nextflow parameter rather than a workflow parameter.\nIt must be specified on the\
+    \ command line or in a `nextflow.config` file.\n\n```console\npixi run \\\n    nf-workflow \\\n  \
+    \      -profile \"local,docker\" \\\n        --input tests/data/basic_input.tsv \\\n        -output-dir\
+    \ results\n```\n\n<details>\n<summary>Click to toggle output directory structure</summary>\n\n\n```console\n\
+    results\n└── {sample_name}\n    ├── {sample_name}_sorted.bam                # Coordinate-sorted BAM\
+    \ file\n    ├── {sample_name}_svpileup.txt              # SvPileup breakpoint candidates\n    ├──\
+    \ {sample_name}_svpileup.bam              # BAM with SV tags from SvPileup\n    ├── {sample_name}_svpileup.aggregate.txt\
+    \    # Aggregated/merged breakpoint pileups\n    └── {sample_name}_svpileup.aggregate.bedpe  # Aggregated\
+    \ pileups in BEDPE format\n```\n\n</details>\n\n### Output File Descriptions\n\n| File | Description\
+    \ |\n|------|-------------|\n| `*_sorted.bam` | Input BAM sorted by genomic coordinates using samtools\
+    \ sort |\n| `*_svpileup.txt` | Candidate structural variant breakpoints identified by [fgsv SvPileup](https://github.com/fulcrumgenomics/fgsv)\
+    \ |\n| `*_svpileup.bam` | BAM file with SV-related tags added by SvPileup |\n| `*_svpileup.aggregate.txt`\
+    \ | Merged breakpoint pileups from [fgsv AggregateSvPileup](https://github.com/fulcrumgenomics/fgsv)\
+    \ |\n| `*_svpileup.aggregate.bedpe` | Aggregated pileups converted to [BEDPE format](https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format)\
+    \ |\n\n## Contributing\n\nSee our [Contributing Guide](docs/CONTRIBUTING.md) for development and testing\
+    \ guidelines.\n\n\n"
+inputs:
+- name: input
+  type: string
+  description: Path to tab-separated file containing information about the samples in the experiment.
+  required: true
+  format: file-path
+  pattern: .*.tsv$
+  group: Main workflow parameters
+config_params: []
+workflows:
+- name: ''
+  docstring: ''
+  file: main.nf
+  line: 19
+  end_line: 42
+  inputs: []
+  outputs: []
+  calls: []
+  is_entry: true
+  source_url: https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/main.nf#L19-L42
+processes:
+- name: AGGREGATE_SV_PILEUP_TO_BEDPE
+  docstring: 'Convert aggregated SvPileup output to BEDPE format using fgsv
+
+    AggregateSvPileupToBedPE.'
+  file: modules/aggregate_sv_pileup_to_bedpe.nf
+  line: 11
+  end_line: 31
+  inputs:
+  - name: val(meta), path(txt)
+    type: tuple
+    description: '`meta`: Map containing sample information (must include ''id''); `txt`: Aggregated SvPileup
+      output file'
+    qualifier: Tuple<Map, Path>
+  outputs:
+  - name: val(meta), file("*_svpileup.aggregate.bedpe")
+    type: tuple
+    description: Tuple of meta and BEDPE format output file
+    emit: bedpe
+  directives: {}
+  source_url: https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/aggregate_sv_pileup_to_bedpe.nf#L11-L31
+- name: AGGREGATE_SV_PILEUP
+  docstring: 'Aggregate and merge pileups that are likely to support the same breakpoint
+
+    using fgsv AggregateSvPileup.'
+  file: modules/aggregate_sv_pileup.nf
+  line: 12
+  end_line: 33
+  inputs:
+  - name: val(meta), path(bam), path(txt)
+    type: tuple
+    description: '`meta`: Map containing sample information (must include ''id''); `bam`: Input BAM file;
+      `txt`: SvPileup breakpoint output file'
+    qualifier: Tuple<Map, Path, Path>
+  outputs:
+  - name: val(meta), file("*_svpileup.aggregate.txt")
+    type: tuple
+    description: Tuple of meta and aggregated SvPileup output file
+    emit: txt
+  directives: {}
+  source_url: https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/aggregate_sv_pileup.nf#L12-L33
+- name: COORDINATE_SORT
+  docstring: Sort a BAM file by genomic coordinates using samtools sort.
+  file: modules/coordinate_sort.nf
+  line: 10
+  end_line: 31
+  inputs:
+  - name: val(meta), path(bam)
+    type: tuple
+    description: '`meta`: Map containing sample information (must include ''id''); `bam`: Input BAM file
+      to be sorted'
+    qualifier: Tuple<Map, Path>
+  outputs:
+  - name: val(meta), file("*_sorted.bam")
+    type: tuple
+    description: Tuple of meta and coordinate-sorted BAM file
+    emit: bam
+  directives: {}
+  source_url: https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/coordinate_sort.nf#L10-L31
+- name: SV_PILEUP
+  docstring: Detect structural variant evidence from a BAM file using fgsv SvPileup.
+  file: modules/sv_pileup.nf
+  line: 11
+  end_line: 33
+  inputs:
+  - name: val(meta), path(bam)
+    type: tuple
+    description: '`meta`: Map containing sample information (must include ''id''); `bam`: Input BAM file'
+    qualifier: Tuple<Map, Path>
+  outputs:
+  - name: val(meta), file("*_svpileup.txt")
+    type: tuple
+    description: Tuple of meta and SvPileup breakpoint output file
+    emit: txt
+  - name: val(meta), file("*_svpileup.bam")
+    type: tuple
+    description: Tuple of meta and SvPileup BAM file
+    emit: bam
+  directives: {}
+  source_url: https://github.com/fulcrumgenomics/nf-fgsv/blob/73e7adf5d96a2031f89519bbb378d8e19954aeb7/modules/sv_pileup.nf#L11-L33
+functions: []