terra_workflow.json

task run_metaMutationalSignatures {
    File vcf_directory_
    String genome_reference
    String 
  
    command {
      docker run --rm -it -v C:\Users\...full_path...\docker_input_test/:/app/input_vcf_dir pp535/metamutationalsigs  --i 'input_vcf_dir' --sigflow --sigfit
        // metaMutatationalSignatures fit ${"-g " + genome_reference} ${"-i " + input_maf} ${"-o results"}
    }
  
    output {
      ## And make the output ./sigflow_result.gz
      File output_compressed="./results.tar.gz/"
    }
  
    runtime {
      docker: "pp535/metamutationalsigs"
         memory: "64 GB"
      disks: "local-disk 128 SSD"    
    }
  }
  
  
  workflow metaMutationalSignatures {
    call run_metaMutationalSignatures
  }