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POC: module yaml restructure #2789

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POC: module yaml restructure #2789

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30 changes: 21 additions & 9 deletions nf_core/components/nfcore_component.py
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Original file line number Diff line number Diff line change
Expand Up @@ -166,15 +166,27 @@ def get_inputs_from_main_nf(self):
log.info(f"Could not find any inputs in {self.main_nf}")
return inputs
input_data = data.split("input:")[1].split("output:")[0]
regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
matches = re.finditer(regex, input_data, re.MULTILINE)
for _, match in enumerate(matches, start=1):
if match.group(3):
input_val = match.group(3).split(",")[0] # handle `files, stageAs: "inputs/*"` cases
inputs.append(input_val)
elif match.group(4):
input_val = match.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases
inputs.append(input_val)
for line in input_data.split("\n"):
theseinputs = []
regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
matches = re.finditer(regex, line)
for _, match in enumerate(matches, start=1):
input_type = None
input_val = None
if match.group(1):
input_type = match.group(1)
if match.group(3):
input_val = match.group(3).split(",")[0] # handle `files, stageAs: "inputs/*"` cases
elif match.group(4):
input_val = match.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases
if input_type and input_val:
theseinputs.append({
input_val: {
"type": input_type
}
})
if len(theseinputs) > 0:
inputs.append(theseinputs)
log.info(f"Found {len(inputs)} inputs in {self.main_nf}")
self.inputs = inputs

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2 changes: 2 additions & 0 deletions nf_core/modules/lint/meta_yml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,8 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
"""

module.get_inputs_from_main_nf()
print(yaml.dump({"input": module.inputs}))
exit()
module.get_outputs_from_main_nf()
# Check if we have a patch file, get original file in that case
meta_yaml = None
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