[e] null model currently does not transfer metadata to the output

[aofarrel]

    ############
    '''
    The follow section is included in the CWL but not the WDL as it appears
    to either be specific to seven bridges or have no purpose, as the WDL lacks
    it yet still MD5s to the output of the SB CWLs. It is included here with 
    additional comments to document what is missing from the WDL.

    In the CWL, inheritMetadata is called on (self, inputs.phenotype_file) as
    an output evaluation for the null model phenotype output.
    So, o1 is the phenotype output, and o2 is the phenotype input file.

    class: InlineJavascriptRequirement
    expressionLib:
    - |2-

        var setMetadata = function(file, metadata) {

            # if there is no metadata in the file then set it to the entirity of metadata
            if (!('metadata' in file))
                file['metadata'] = metadata;

            # else, dont do a wholesale overwrite, instead just add new keys/overwrite confliciting keys  
            else {
                for (var key in metadata) {
                    file['metadata'][key] = metadata[key];
                }
            }
            return file
        };

        var inheritMetadata = function(o1, o2) {
            var commonMetadata = {};

            # if not an array, make it an array
            if (!Array.isArray(o2)) {
                o2 = [o2]
            }
            for (var i = 0; i < o2.length; i++) {
                var example = o2[i]['metadata'];
                for (var key in example) {

                    # on the zeroeth iteration of the outer loop,
                    # give the empty set keys-value pairs matching
                    # that of o2s zeroeth metadata 
                    if (i == 0)
                        commonMetadata[key] = example[key];

                    # on all other iterations of the outer loop,
                    # delete stuff that... does not exist???
                    else {
                        if (!(commonMetadata[key] == example[key])) {
                            delete commonMetadata[key]
                        }
                    }
                }
            }
            if (!Array.isArray(o1)) {
                # if not an array, set metadata based on commonMetadata
                # (which itself is based on o2s metadata, kind of)
                o1 = setMetadata(o1, commonMetadata)
            } else {
                # if it is an array, add common metadata to what it already has
                for (var i = 0; i < o1.length; i++) {
                    o1[i] = setMetadata(o1[i], commonMetadata)
                }
            }
            return o1;
        };
    '''
    ############

[aofarrel]

If the transfer is actually to the inputs, then the way the parameter file is used by the next task finally makes sense.

[aofarrel]

We spoke with Stephanie about this and determined that the metadata inheritance code is SB specific. It also does not appear to have any actual difference on the phenotypic outputs, as they continue to MD5 to each other across SB and local WDL.