ruchim

task regression {
    input {
        String phecode
        String phecode_directory
        String plink
        File covars        
    }
    
    File phecode_file = phecode_directory + phecode + ".tsv"
    

ruchim

version 1.0 

workflow test_workflow_functions {
  File f = "gs://path-to-something/object"
  Float s = size(f)
}

ruchim

{}

ruchim

{
  "id": "UUID",
  "name": "TwistTCAP_POC_v8",
  "description": "Testing things out...",
  "defaultProfileId": null,
  "dataProject": null,
  "defaultSnapshotId": null,
  "schema": {
    "tables": [
      {

ruchim

{
  "defaultProfileId": "390e7a85-d47f-4531-b612-165fc977d3bd",
  "description": "example data repo dataset",
  "name": "example_demo_dataset",
  "schema": {
    "relationships": [
      {
        "from": {
          "column": "participant_id",
          "table": "sample"

ruchim

## - Reference genome must be Hg38 with ALT contigs
##
## Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
## For program versions, see docker containers.
##
## LICENSING :
## This script is released under the WDL source code license (BSD-3) (see LICENSE in
## https://github.com/broadinstitute/wdl). Note however that the programs it calls may
## be subject to different licenses. Users are responsible for checking that they are
## authorized to run all programs before running this script. Please see the docker

ruchim

workflow test_gpu_wf {
	
	call test_gpu {}
}

task test_gpu {
	command { nvidia-smi }
	runtime { 
	    gpuType: "nvidia-tesla-k80"
    	gpuCount: 1

ruchim

## Copyright Broad Institute, 2018
## 
## This WDL pipeline implements data pre-processing according to the GATK Best Practices 
## (June 2016).  
##
## Requirements/expectations :
## - Pair-end sequencing data in unmapped BAM (uBAM) format
## - One or more read groups, one per uBAM file, all belonging to a single sample (SM)
## - Input uBAM files must additionally comply with the following requirements:
## - - filenames all have the same suffix (we use ".unmapped.bam")

ruchim

{
  "wf_hello.print.inFile": "gs://rm-dev/a.txt"
}

ruchim

task print {
  File inFile
  command {
    cat ${inFile}
  }
  output {
    String contents = read_string(stdout())
  }
  runtime {
    docker: "ubuntu@sha256:71cd81252a3563a03ad8daee81047b62ab5d892ebbfbf71cf53415f29c130950"