Pass inputs to subworkflow in inputs.json

I am trying to run a workflow with a subworkflow that has some workflow level inputs. Somethign along the lines of

Workflow subWorkflow {

File f
String s
...
...
}

import "file/path/subworkflow.wdl" as sub

workflow root {
call sub.subWorkflow as aliasSub
}

When I try to pass the values for File f and String s from the inputs json I get an failure message.

To make sure I was giving the workflow the correct inputs json I first ran it with bad inputs on purpose and got expected failures

status: "Failed",
failures: [
{
causedBy: [
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.ref_pac' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.agg_preemptible_tries' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.ref_ann' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.wgs_coverage_interval_list' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.ref_fasta_index' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.unmapped_bam_suffix' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.contamination_sites_ud' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.ref_amb' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.preemptible_tries' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.ref_sa' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.known_indels_sites_VCFs' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.contamination_sites_mu' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.ref_alt' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.ref_bwt' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.known_indels_sites_indices' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.ref_dict' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.contamination_sites_bed' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.ref_fasta' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.dbSNP_vcf_index' not specified."
},
{
causedBy: [ ],
message: "Required workflow input 'SomaticRoot.TumorAlignment.dbSNP_vcf' not specified."
}
],
message: "Workflow input processing failed"
}
],

But once I filled these out in my inputs json I then got this error

[
{
causedBy: [
{
causedBy: [ ],
message: "Missing inputs for subworkflow call SomaticRoot.TumorAlignment at index None: read_length, ref_fasta, agg_preemptible_tries, ref_dict, haplotype_database_file, ref_alt, ref_ann, known_indels_sites_indices, dbSNP_vcf, ref_sa, dbSNP_vcf_index, unmapped_bam_suffix, ref_amb, contamination_sites_ud, contamination_sites_bed, ref_bwt, ref_fasta_index, increase_disk_size, fingerprint_genotypes_file, preemptible_tries, known_indels_sites_VCFs, contamination_sites_mu, wgs_coverage_interval_list, ref_pac."
}
],
message: "Couldn't resolve all inputs for SomaticRoot.TumorAlignment at index None."
}
],

I think I’m passing in everything correctly but it could be an error on my part as well.

[eganlohman]

@ruchim - I know you said 3-6 months from Nov. Just curious if this issue has been picked up yet for active dev? Percolating sub-workflow task inputs all the way up to the root workflow is a major pain.

[rhpvorderman]

I ran in this issue this week and it requires some quite nasty and ugly workarounds. So it would be great if this could be fixed. What I can grok from the code in Cromwell is that the node structure only considers tasks as ExternalInputNode. These have inputs that can be overwritten. Other nodes may be considered OuterGraphInputNode. Basically everything that is not an ExternalInputNode can not be considered for options that can be overridden.

I feel there is a lot of technical decisions being made in this piece of code. Without knowing all the reasons why decisions are made it will be very hard to solve this in a PR for an outside contributor. It is hard to find the place in which to edit code in this case. I would love to take some work of cromwell’s developers hands, but I need more guidance to do so. @ruchim can I help out in any way in the effort to solve this issue?