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Can the order of the inputs and outputs to a method config be displayed in a rational order?

yfarjounyfarjoun Broad InstituteDev ✭✭✭

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.

Best Answer


  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    A similar request, but also a very good suggestion, and I have also struggled with this random order. I believe this may have been requested before, and if so, I'll add a note to reprioritize the issue. If not, I will create a new ticket.

  • yfarjounyfarjoun Broad InstituteDev ✭✭✭

    I think that it's in the "Nice to Have" category, not "Problematic behavior"category.


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