Gather step fails when sex-specific analysis is disabled for clustered endpoints

[Lipastomies]

In step2, the combination of 1) multiple clustered endpoints and 2) disabling sex-specific analysis causes the step2 pipeline to fail.

It works like this:

1. when we disable sex-specific analysis, step2 step creates one sex-specific placeholder. When running clustered endpoints, there are instead n_endpoints sex-specific files.

if [[ "${run_sex_specific}" == "true" ]];
        then
for p in ${sep=" " phenolist}; do
# ...
done
# ...
fi
else
          ## sex specific analyses disabled but create the file so gather step is straightforward to implement
          touch ${prefix}"NOT_DONE.sex_spec.gz"

2. when taking outputs for gathering step, we take the Array[Array[File]] of sex-specific files, of size N chunks * N clustered endpoints, transpose it, and then index it per endpoint. So indexing N clustered endpoints* N chunks array with each endpoint.

Array[Array[String]] pheno_results_sex = transpose(step2.sex_specifix)
scatter (pheno_result_idx in range(length(pheno_results))) {
        call gather {
            input: is_binary=is_binary, files=pheno_results[pheno_result_idx],
              sex_files = pheno_results_sex[pheno_result_idx], docker=docker
        }
        call summary {
            input: input_file=gather.pheweb, docker=docker
        }
    }

3. The error is in the fact that when skipping sex-specific analysis, we create only N chunks*1 array of arrays, and the gather step requires N chunks * N endpoints, we get array indexing into nonexistent indices.

I'll fix this for R12 with an if-else in the gather step, replacing the sex-specific files with an empty array if no sex-specific analysis was done.

        Array[String] sex_files = if run_sex_specific then pheno_results_sex[pheno_result_idx] else []
        call gather {
            input: is_binary=is_binary, files=pheno_results[pheno_result_idx],
              sex_files = sex_files, docker=docker
        }