Bonus: review the CWL recommended practices checklist

[mr-c]

http://www.commonwl.org/user_guide/rec-practices/

• No type: string parameters for names of input or reference files/directories; use type: File or type: Directory as appropriate.
• Include a license that allows for re-use by anyone, e.g. Apache 2.0. Example of license inclusion.
• Include attribution information for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like ORCID.
• In tool descriptions, list dependencies using short name(s) under SoftwareRequirement.
• Include SciCrunch identifiers for dependencies in https://identifiers.org/rrid/RRID:SCR_NNNNNN format.
• All input and output identifiers should reflect their conceptual identity. Use informative names like unaligned_sequences, reference_genome, phylogeny, or aligned_sequences instead of foo_input, foo_file, result, input, output, and so forth.
• In tool descriptions, include a list of version(s) of the tool that are known to work with this description under SoftwareRequirement.
• format should be specified for all input and output Files. Bioinformatics tools should use format identifiers from EDAM. See also iana:text/plain, iana:text/tab-separated-values with $namespaces: { iana: "https://www.iana.org/assignments/media-types/" }. Full IANA media type list(also known as MIME types). For non-bioinformatics tools use or build an appropriate ontology/controlled vocabulary in the same way.
• Mark all input and output Files that are read from or written to in a streaming compatible way (only once, no random-access), as streamable: true.
• Each CommandLineTool description should focus on a single operation only, even if the (sub)command is capable of more. Don’t overcomplicate your tool descriptions with options that you don’t need/use.
• Custom types should be defined with one external YAML per type definition for re-use.
• Include a top level short label summarising the tool/workflow.
• If useful, include a top level doc as well. This should provide a longer, more detailed description than was provided in the top level label (see above).
• Use type: enum instead of type: string for elements with a fixed list of valid values.
• Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating File names and paths? Consider whether one of the built-in in File properties like basename, nameroot, nameext, etc, could be used instead.
• Give the tool description to a colleague (preferably at a different institution) to test and provide feedback.