Issue passing an output directory path to blob container as an command line argument

[mdanner93]

Hi everyone,

I set up CromwellOnAzure but I have a problem passing a directory path as an output during workflows
e.g. running a GenomeDBImport task on Azure:

version 1.0

workflow GenomicsDBImport {
    input {
    File input_patient
    File input_mother 
    File input_father
    File bed_file
    Array[File] reads
    String output_dir
    String gatk_docker = "broadinstitute/gatk:latest"
    String gatk_path = "/gatk/gatk"
    }
    

    call DBImport { 
        input:
            input_patient = input_patient,
            input_mother = input_mother,
            input_father = input_father,
            bed_file = bed_file,
            reads = reads,
            output_dir = output_dir,
            docker = gatk_docker,
            gatk_path = gatk_path
    }
}

task DBImport {
    input {
    # Command Parameters
    File input_patient
    File input_mother 
    File input_father
    File bed_file
    Array[File] reads
    String gatk_path
    String output_dir
    
    # Runtime Parameters
    String docker
    Int addtional_disk_space_gb = 10
    Int machine_mem_gb = 64
    Int preemptible_attempts = 3
    
    Int disk_space_gb = 40 + addtional_disk_space_gb
    }

    command {
        ~{gatk_path} --java-options "-Xmx32g -Xms32g" GenomicsDBImport \
        -V ~{input_patient} \
        -V ~{input_mother} \
        -V ~{input_father} \
        --genomicsdb-workspace-path ~{output_dir} \
        --read-index ~{sep="," reads} \
        -L ~{bed_file} --merge-input-intervals true \
        --max-num-intervals-to-import-in-parallel 70000 \
        --verbosity DEBUG
    }

    runtime {
        docker: docker
        memory: machine_mem_gb + " GB"
        disk: disk_space_gb + " GB"
        preemptible: true
        maxRetries: preemptible_attempts
    }

    output {
        String output_db = "${output_dir}"
    }

}

Leads to the following error:

A USER ERROR has occurred: Error creating GenomicsDB workspace: https://mydatalake.blob.core.windows.net/genomicsdb/test/genomicsdb

I am really looking forward for your help.

Many thanks in advance!