+ 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 +212,24 @@ 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.
+
+ The Nextflow LSP may represent unknown or unresolved types as ``?``.
+
+ 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 +250,30 @@ 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 ""
@@ -205,9 +300,92 @@ 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
+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.
+
+ 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)
+ 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)
+ 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.
@@ -284,3 +462,79 @@ def is_code_block(text: str) -> bool:
return True
return False
+
+
+def enrich_outputs_from_source(
+ outputs: list[ParsedOutput],
+ source: str,
+ process_name: str,
+) -> list[ParsedOutput]:
+ """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 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
+ 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: 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)
+ 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")
+ 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 = _OUTPUT_SECTION_RE.search(proc_body)
+ 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/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 ``Title
`` to::
+
+
+ Title¶
+
- Transforms Title
to:
- Title¶
+ 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])>(.+?)", 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:
diff --git a/src/nf_docs/templates/html.html b/src/nf_docs/templates/html.html
index f483d52..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 @@ Pipeline Inputs
>
{{ inp.format }}
+ {% endif %} {% if inp.pattern %}
+
+ Pattern: {{ inp.pattern }}
+
{% endif %} {% if inp.required %}
Inputs (take)
>{{ inp.name|wbr }}
- {{ inp.description or '-' }} |
+
+ {% if inp.description %}
+ {{ inp.description|markdown }}
+ {% else %}-{% endif %}
+ |
{% endfor %} {% endif %}
@@ -1708,7 +1722,11 @@ Outputs (emit)
>{{ out.name|wbr }}
- {{ out.description or '-' }} |
+
+ {% if out.description %}
+ {{ out.description|markdown }}
+ {% else %}-{% endif %}
+ |
{% endfor %} {% endif %}
@@ -1964,7 +1982,11 @@ Inputs
>{{ inp.type|wbr }}
- {{ inp.description or '-' }} |
+
+ {% if inp.description %}
+ {{ inp.description|markdown }}
+ {% else %}-{% endif %}
+ |
{% endfor %} {% endif %}
@@ -2040,7 +2062,11 @@ Outputs
>
{% else %}-{% endif %}
- {{ out.description or '-' }} |
+
+ {% if out.description %}
+ {{ out.description|markdown }}
+ {% else %}-{% endif %}
+ |
{% endfor %} {% endif %}
@@ -2182,7 +2208,11 @@ Parameters
>{{ p.name|wbr }}
- {{ p.description or '-' }} |
+
+ {% if p.description %}
+ {{ p.description|markdown }}
+ {% else %}-{% endif %}
+ |
{% if p.default is not none %}
:not(:last-child)){--tw-space-y-reverse:0;margin-block-start:calc(calc(var(--spacing)*.5)*var(--tw-space-y-reverse));margin-block-end:calc(calc(var(--spacing)*.5)*calc(1 - var(--tw-space-y-reverse)))}:where(.space-y-1>:not(:last-child)){--tw-space-y-reverse:0;margin-block-start:calc(calc(var(--spacing)*1)*var(--tw-space-y-reverse));margin-block-end:calc(calc(var(--spacing)*1)*calc(1 - var(--tw-space-y-reverse)))}:where(.space-y-3>:not(:last-child)){--tw-space-y-reverse:0;margin-block-start:calc(calc(var(--spacing)*3)*var(--tw-space-y-reverse));margin-block-end:calc(calc(var(--spacing)*3)*calc(1 - var(--tw-space-y-reverse)))}.truncate{text-overflow:ellipsis;white-space:nowrap;overflow:hidden}.overflow-x-auto{overflow-x:auto}.overflow-y-auto{overflow-y:auto}.rounded{border-radius:.25rem}.rounded-full{border-radius:3.40282e38px}.rounded-lg{border-radius:var(--radius-lg)}.rounded-md{border-radius:var(--radius-md)}.border{border-style:var(--tw-border-style);border-width:1px}.border-t{border-top-style:var(--tw-border-style);border-top-width:1px}.border-r{border-right-style:var(--tw-border-style);border-right-width:1px}.border-b{border-bottom-style:var(--tw-border-style);border-bottom-width:1px}.border-l{border-left-style:var(--tw-border-style);border-left-width:1px}.border-l-4{border-left-style:var(--tw-border-style);border-left-width:4px}.border-primary{border-color:var(--color-primary)}.border-slate-200{border-color:var(--color-slate-200)}.border-slate-300{border-color:var(--color-slate-300)}.bg-black\/50{background-color:#00000080}@supports (color:color-mix(in lab, red, red)){.bg-black\/50{background-color:color-mix(in oklab,var(--color-black)50%,transparent)}}.bg-green-100{background-color:var(--color-green-100)}.bg-primary{background-color:var(--color-primary)}.bg-primary-light{background-color:var(--color-primary-light)}.bg-purple-100{background-color:var(--color-purple-100)}.bg-red-100{background-color:var(--color-red-100)}.bg-slate-50{background-color:var(--color-slate-50)}.bg-slate-100{background-color:var(--color-slate-100)}.bg-slate-200{background-color:var(--color-slate-200)}.bg-white{background-color:var(--color-white)}.p-1\.5{padding:calc(var(--spacing)*1.5)}.p-3{padding:calc(var(--spacing)*3)}.p-4{padding:calc(var(--spacing)*4)}.p-6{padding:calc(var(--spacing)*6)}.px-1\.5{padding-inline:calc(var(--spacing)*1.5)}.px-2{padding-inline:calc(var(--spacing)*2)}.px-3{padding-inline:calc(var(--spacing)*3)}.px-4{padding-inline:calc(var(--spacing)*4)}.py-0\.5{padding-block:calc(var(--spacing)*.5)}.py-1{padding-block:calc(var(--spacing)*1)}.py-1\.5{padding-block:calc(var(--spacing)*1.5)}.py-2{padding-block:calc(var(--spacing)*2)}.py-8{padding-block:calc(var(--spacing)*8)}.pt-3{padding-top:calc(var(--spacing)*3)}.pt-4{padding-top:calc(var(--spacing)*4)}.pt-14{padding-top:calc(var(--spacing)*14)}.pb-2{padding-bottom:calc(var(--spacing)*2)}.pb-6{padding-bottom:calc(var(--spacing)*6)}.text-center{text-align:center}.text-left{text-align:left}.font-mono{font-family:var(--font-mono)}.font-sans{font-family:var(--font-sans)}.text-2xl{font-size:var(--text-2xl);line-height:var(--tw-leading,var(--text-2xl--line-height))}.text-3xl{font-size:var(--text-3xl);line-height:var(--tw-leading,var(--text-3xl--line-height))}.text-lg{font-size:var(--text-lg);line-height:var(--tw-leading,var(--text-lg--line-height))}.text-sm{font-size:var(--text-sm);line-height:var(--tw-leading,var(--text-sm--line-height))}.text-xl{font-size:var(--text-xl);line-height:var(--tw-leading,var(--text-xl--line-height))}.text-xs{font-size:var(--text-xs);line-height:var(--tw-leading,var(--text-xs--line-height))}.leading-relaxed{--tw-leading:var(--leading-relaxed);line-height:var(--leading-relaxed)}.font-bold{--tw-font-weight:var(--font-weight-bold);font-weight:var(--font-weight-bold)}.font-medium{--tw-font-weight:var(--font-weight-medium);font-weight:var(--font-weight-medium)}.font-normal{--tw-font-weight:var(--font-weight-normal);font-weight:var(--font-weight-normal)}.font-semibold{--tw-font-weight:var(--font-weight-semibold);font-weight:var(--font-weight-semibold)}.tracking-wide{--tw-tracking:var(--tracking-wide);letter-spacing:var(--tracking-wide)}.text-green-700{color:var(--color-green-700)}.text-primary{color:var(--color-primary)}.text-primary-dark{color:var(--color-primary-dark)}.text-purple-700{color:var(--color-purple-700)}.text-red-600{color:var(--color-red-600)}.text-slate-300{color:var(--color-slate-300)}.text-slate-400{color:var(--color-slate-400)}.text-slate-500{color:var(--color-slate-500)}.text-slate-600{color:var(--color-slate-600)}.text-slate-700{color:var(--color-slate-700)}.text-slate-800{color:var(--color-slate-800)}.text-white{color:var(--color-white)}.uppercase{text-transform:uppercase}.italic{font-style:italic}.no-underline{text-decoration-line:none}.shadow-xl{--tw-shadow:0 20px 25px -5px var(--tw-shadow-color,#0000001a),0 8px 10px -6px 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(hover:hover){.hover\:border-primary:hover{border-color:var(--color-primary)}.hover\:bg-slate-50:hover{background-color:var(--color-slate-50)}.hover\:bg-slate-100:hover{background-color:var(--color-slate-100)}.hover\:text-primary:hover{color:var(--color-primary)}.hover\:text-slate-600:hover{color:var(--color-slate-600)}.hover\:text-slate-900:hover{color:var(--color-slate-900)}.hover\:underline:hover{text-decoration-line:underline}.hover\:opacity-80:hover{opacity:.8}}.focus\:border-transparent:focus{border-color:#0000}.focus\:ring-2:focus{--tw-ring-shadow:var(--tw-ring-inset,)0 0 0 calc(2px + var(--tw-ring-offset-width))var(--tw-ring-color,currentcolor);box-shadow:var(--tw-inset-shadow),var(--tw-inset-ring-shadow),var(--tw-ring-offset-shadow),var(--tw-ring-shadow),var(--tw-shadow)}.focus\:ring-primary:focus{--tw-ring-color:var(--color-primary)}.focus\:outline-none:focus{--tw-outline-style:none;outline-style:none}@media (min-width:40rem){.sm\:inline{display:inline}}@media (min-width:48rem){.md\:ml-56{margin-left:calc(var(--spacing)*56)}.md\:block{display:block}.md\:hidden{display:none}.md\:w-64{width:calc(var(--spacing)*64)}.md\:p-8{padding:calc(var(--spacing)*8)}.md\:px-6{padding-inline:calc(var(--spacing)*6)}}@media (min-width:64rem){.lg\:mr-64{margin-right:calc(var(--spacing)*64)}.lg\:block{display:block}.lg\:p-12{padding:calc(var(--spacing)*12)}}}@property --tw-translate-x{syntax:"*";inherits:false;initial-value:0}@property --tw-translate-y{syntax:"*";inherits:false;initial-value:0}@property --tw-translate-z{syntax:"*";inherits:false;initial-value:0}@property --tw-rotate-x{syntax:"*";inherits:false}@property --tw-rotate-y{syntax:"*";inherits:false}@property --tw-rotate-z{syntax:"*";inherits:false}@property --tw-skew-x{syntax:"*";inherits:false}@property --tw-skew-y{syntax:"*";inherits:false}@property --tw-space-y-reverse{syntax:"*";inherits:false;initial-value:0}@property --tw-border-style{syntax:"*";inherits:false;initial-value:solid}@property --tw-leading{syntax:"*";inherits:false}@property --tw-font-weight{syntax:"*";inherits:false}@property --tw-tracking{syntax:"*";inherits:false}@property --tw-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-shadow-color{syntax:"*";inherits:false}@property --tw-shadow-alpha{syntax:"";inherits:false;initial-value:100%}@property --tw-inset-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-inset-shadow-color{syntax:"*";inherits:false}@property --tw-inset-shadow-alpha{syntax:"";inherits:false;initial-value:100%}@property --tw-ring-color{syntax:"*";inherits:false}@property --tw-ring-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-inset-ring-color{syntax:"*";inherits:false}@property --tw-inset-ring-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-ring-inset{syntax:"*";inherits:false}@property --tw-ring-offset-width{syntax:"";inherits:false;initial-value:0}@property --tw-ring-offset-color{syntax:"*";inherits:false;initial-value:#fff}@property --tw-ring-offset-shadow{syntax:"*";inherits:false;initial-value:0 0 #0000}@property --tw-duration{syntax:"*";inherits:false}@property --tw-ease{syntax:"*";inherits:false}
\ No newline at end of file
diff --git a/tests/test_extractor.py b/tests/test_extractor.py
index 3339e66..535b1d8 100644
--- a/tests/test_extractor.py
+++ b/tests/test_extractor.py
@@ -160,3 +160,113 @@ 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):
+ """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
+
+ output:
+ txt
+ bam
+}
+"""
+ 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):
+ """Returns empty when process not found in source."""
+ from nf_docs.extractor import _parse_groovydoc_from_source
+
+ docstring, params = _parse_groovydoc_from_source(
+ "process OTHER { script: '' }\n", "MISSING"
+ )
+ 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", {}) == ""
diff --git a/tests/test_nf_parser.py b/tests/test_nf_parser.py
new file mode 100644
index 0000000..f02d47e
--- /dev/null
+++ b/tests/test_nf_parser.py
@@ -0,0 +1,644 @@
+"""Tests for the Nextflow code parser."""
+
+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,
+)
+
+
+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"""
+ result = _parse_single_input("(meta, bam): Tuple")
+ assert result is not None
+ assert result.type == "tuple"
+ assert result.name == "val(meta), path(bam)"
+ assert result.qualifier == "Tuple"
+
+ def test_typed_tuple_three_elements(self):
+ """Typed tuple: (meta, bam, txt): Tuple"""
+ result = _parse_single_input("(meta, bam, txt): Tuple")
+ assert result is not None
+ assert result.type == "tuple"
+ assert result.name == "val(meta), path(bam), path(txt)"
+ assert result.qualifier == "Tuple"
+
+ def test_typed_tuple_all_vals(self):
+ """Typed tuple with all value types."""
+ result = _parse_single_input("(name, count): Tuple")
+ assert result is not None
+ assert result.type == "tuple"
+ assert result.name == "val(name), val(count)"
+ assert result.qualifier == "Tuple"
+
+ 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_typed_tuple_with_question_mark_type(self):
+ """Typed tuple with ? (unresolved) type from LSP: (meta, bam): Tuple"""
+ result = _parse_single_input("(meta, bam): Tuple")
+ assert result is not None
+ assert result.type == "tuple"
+ assert result.name == "val(meta), path(bam)"
+ assert result.qualifier == "Tuple"
+
+ def test_typed_tuple_three_with_question_mark(self):
+ """Typed 3-tuple with ? type: (meta, bam, txt): Tuple"""
+ result = _parse_single_input("(meta, bam, txt): Tuple")
+ assert result is not None
+ assert result.type == "tuple"
+ assert result.name == "val(meta), path(bam), path(txt)"
+ assert result.qualifier == "Tuple"
+
+ 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")
+ 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"
+
+
+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_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
+ 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
+
+ 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"
+ 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
+
+ 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
+
+ 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"
+
+ 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
+
+ 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"
+ # 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
+
+ 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."""
+
+ 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 == []
+
+
+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
+
+ 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):
+ """Bare emit names are replaced with full declarations from source."""
+ bare_outputs = [
+ ParsedOutput(name="txt", type="", emit="txt"),
+ ParsedOutput(name="bam", type="", emit="bam"),
+ ]
+ result = enrich_outputs_from_source(bare_outputs, self.SV_PILEUP_SOURCE, "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):
+ """Outputs that already have a type are left untouched."""
+ qualified_outputs = [
+ ParsedOutput(name="val(meta), path(*.html)", type="tuple", emit="html"),
+ ]
+ 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_process_not_found_returns_originals(self):
+ """If the process name isn't in the source, return outputs unchanged."""
+ bare_outputs = [ParsedOutput(name="txt", type="", emit="txt")]
+ 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):
+ """Only bare outputs whose emit matches a source declaration are enriched."""
+ outputs = [
+ ParsedOutput(name="txt", type="", emit="txt"),
+ ParsedOutput(name="unknown", type="", emit="unknown"),
+ ]
+ 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):
+ """Named simple output: versions = path("versions.yml")."""
+ 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, "SIMPLE")
+
+ assert result[0].emit == "versions"
+ assert result[0].type == "path"
+ assert result[0].name == "versions.yml"
| 
+
+