This is a similar request to a previous one of mine, but it's different.
In a method config the order of the inputs (and outputs) is seemingly arbitrary:
QCAndPrePhase.dataset_fam: (File)this.fam
QCAndPrePhase.reference_fasta: (File)workspace.reference_fasta
QCAndPrePhase.dbSnp_vcf_index: (File)workspace.dbSnp_vcf_index
QCAndPrePhase.reference_dict: (File)workspace.reference_dict
QCAndPrePhase.reference_index: (File)workspace.reference_index
QCAndPrePhase.dataset_bed: (File)this.bed
QCAndPrePhase.dbSnp_vcf: (File)workspace.dbSnp_vcf
QCAndPrePhase.genetic_maps_eagle: (File)workspace.genetic_map_eagle
QCAndPrePhase.dataset_bim: (File)this.bim
QCAndPrePhase.plink_frq: (File)workspace.panel_plink_frq
In this case, I think that the order in the WDL is the reasonable way to implement because the author of the WDL can control how it will be presented. for example, put the dbSnp_vcf right before dbSnp_vcf_index or putting reference_fasta first, then reference_dict and then reference_index.