YAML format samplesheets are not properly vaildated

[awgymer]

Discovered as a side effect of #120

yaml format samplesheets are currently not actually vaildated by the validateFile:

nf-validation/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy

Lines 188 to 198 in ac5812a

	if(fileType == "yaml"){
	fileContent = new Yaml().load((samplesheetFile.text))
	}
	else {
	Map types = variableTypes(schemaFile.toString(), baseDir)
	fileContent = samplesheetFile.splitCsv(header:true, strip:true, sep:delimiter)
	fileContentCasted = castToType(fileContent, types)
	}
	if (validateFile(false, samplesheetFile.toString(), fileContentCasted, schemaFile.toString(), baseDir, s3PathCheck)) {
	log.debug "Validation passed: '$samplesheetFile' with '$schemaFile'"
	}

and

nf-validation/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy

Lines 416 to 426 in ac5812a

	if(fileType == "yaml"){
	fileContent = new Yaml().load((file_path.text))
	}
	else {
	Map types = variableTypes(schema_name, baseDir)
	fileContent = file_path.splitCsv(header:true, strip:true, sep:delimiter)
	fileContentCasted = castToType(fileContent, types)
	}
	if (validateFile(useMonochromeLogs, key, fileContentCasted, schema_name, baseDir, s3PathCheck)) {
	log.debug "Validation passed: '$key': '$file_path' with '$schema_name'"
	}

This doesn't throw an error but an empty list is passed to validateFile in the yaml case instead of the fileContent.

The fix should be as simple as switching to fileContentCasted = new Yaml().load((samplesheetFile.text)).

[mirpedrol]

Fixed by #124, thanks!