Module linting: refactor parsing of input channel names.

No more split, regexes FTW!
Fixes nf-core#1542

CHANGELOG.md

@@ -29,6 +29,7 @@
 - Add a new command `nf-core modules mulled` which can generate the name for a multi-tool container image.
 - Add a new command `nf-core modules test` which runs pytests locally.
 - Linting now recognised `shell` blocks to avoid error `when: condition has too many lines` ([#1557](https://github.com/nf-core/tools/issues/1557))
+- Linting: fix error when using comments after `input` tuple lines ([#1542](https://github.com/nf-core/tools/issues/1542))
 
 ## [v2.3.2 - Mercury Vulture Fixed Formatting](https://github.com/nf-core/tools/releases/tag/2.3.2) - [2022-03-24]
 

nf_core/modules/lint/main_nf.py

@@ -80,7 +80,7 @@ def main_nf(module_lint_object, module):
  if state == "process" and not _is_empty(module, l):
  process_lines.append(l)
  if state == "input" and not _is_empty(module, l):
- inputs += _parse_input(module, l)
+ inputs.extend(_parse_input(module, l))
  if state == "output" and not _is_empty(module, l):
  outputs += _parse_output(module, l)
  outputs = list(set(outputs)) # remove duplicate 'meta's
@@ -242,7 +242,9 @@ def check_process_section(self, lines):
  else:
  # Check that required version is available at all
  if bioconda_version not in response.get("versions"):
- self.failed.append(("bioconda_version", "Conda package had unknown version: `{}`", self.main_nf))
+ self.failed.append(
+ ("bioconda_version", f"Conda package had unknown version: `{bioconda_version}`", self.main_nf)
+ )
  continue # No need to test for latest version, continue linting
  # Check version is latest available
  last_ver = response.get("latest_version")
@@ -260,26 +262,41 @@ def check_process_section(self, lines):
  return False
 
 
-def _parse_input(self, line):
- input = []
+def _parse_input(self, line_raw):
+ """
+ Return list of input channel names from an input line.
+
+ If more than one elements in channel should work with both of:
+ tuple val(meta), path(reads)
+ tuple val(meta), path(reads, stageAs: "input*/*")
+
+ If using a tuple, channel names must be in (parentheses)
+ """
+ inputs = []
+ # Remove comments and trailing whitespace
+ line, *_ = line_raw.partition("//")
  line = line.strip()
+ # Tuples with multiple elements
  if "tuple" in line:
- # If more than one elements in channel should work with both of:
- # e.g. tuple val(meta), path(reads)
- # e.g. tuple val(meta), path(reads, stageAs: "input*/*")
- line = line.replace("tuple", "")
- line = line.replace(" ", "")
- for idx, elem in enumerate(line.split(")")):
- if elem:
- elem = elem.split("(")[1]
- elem = elem.split(",")[0].strip()
- input.append(elem)
+ matches = re.findall("\((\w+)\)", line)
+ if matches:
+ inputs.extend(matches)
+ else:
+ self.failed.append(
+ (
+ "main_nf_input_tuple",
+ f"Found tuple but no channel names: `{line}`",
+ self.main_nf,
+ )
+ )
+ # Single element inputs
  else:
  if "(" in line:
- input.append(line.split("(")[1].replace(")", ""))
+ match = re.search("\((\w+)\)", line)
+ inputs.append(match.group(1))
  else:
- input.append(line.split()[1])
- return input
+ inputs.append(line.split()[1])
+ return inputs
 
 
 def _parse_output(self, line):