ruchim

backend {
  # Override the default backend.
  #default = "LocalWithDocker"

  # The list of providers.
  providers {

    # The local provider is included by default in the reference.conf. This is an example.

    # Define a new backend provider.

ruchim

## This is the TopMed alignment workflow WDL for the workflow code located here:
## https://github.com/statgen/docker-alignment
##
## NOTE:  
## The reference genome files to use are located here:
## ftp://share.sph.umich.edu/gotcloud/ref/hs38DH-db142-v1.tgz
##
## You can get the dbSNP reference files that the post align task uses at:
## gs://topmed-irc-share/resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz
## gs://topmed-irc-share/resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi

ruchim

backend {
  # Override the default backend.
  default = "LocalExample"

  # The list of providers.
  providers {

    # The local provider is included by default in the reference.conf. This is an example.

    # Define a new backend provider.

ruchim

cwlVersion: v1.0
class: Workflow

label: "Hello World"
doc: "Outputs a message using echo"

inputs: []

requirements:
  - class: DockerRequirement

ruchim

workflow HelloWorld {
  call echo {}
}

task echo {
  command { echo hello world! }
  runtime {
    docker: "ubuntu:latest"
  }
  output {

ruchim

#!/bin/bash
echo ==================================
echo =========== MONITORING ===========
echo ==================================
echo --- General Information ---
echo \#CPU: $(nproc)
echo Total Memory: $(free -h | grep Mem | awk '{ print $2 }')
echo Total Disk space: $(df -h | grep cromwell_root | awk '{ print $2}')
echo 
echo --- Runtime Information ---

ruchim

include required(classpath("application"))

google {

  application-name = "cromwell"

  auths = [
    {
      name = "application-default"
      scheme = "application_default"