nvnieuwk / nf-samplesheet-conversion Goto Github PK

• Extract helper methods for repetitive or complex logic. For example, the code that checks the header fields could be extracted into a separate method that takes the row and schema as arguments.
• Use meaningful variable and method names. For example, instead of using row or field, use sample and schemaField respectively.
• Use Groovy's built-in type inference to eliminate unnecessary type declarations. For example, you can use def instead of def ArrayList
• Use Groovy's ternary operator to make the code more readable and concise.
• Use Groovy's switch statement instead of nested if statements for better readability and maintainability.
• Avoid unnecessary string concatenation, you can use groovy's multiline string to make it more readable.
• Try to use groovy's collection operations like filter, map, reduce, etc to make it more readable.
• Add proper documentation and comments to make the code more readable and maintainable.
• Use with statements to reduce the number of dot notation calls.
• You could also use the groovy-lint tool to get more suggestions on how to improve your code.

Used in nf-core/genomeassembler: https://github.com/nf-core/taxprofiler/blob/donotdelete-pep-backup/subworkflows/local/input_check.nf

https://json-schema.org/understanding-json-schema/index.html

https://github.com/pepkit/eido

Add a section to the schema which defines which fields are dependent on other fields.

e.g. no-duplicate lane IDs within a single sample name

The files fetched from the samplesheet are of class java.io.File instead of sun.nio.fs.UnixPath. Modules are unable to use file of the current class