ruchim

include required(classpath("application"))

google {

  application-name = "cromwell"

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

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

workflow HelloWorld {
  call echo {}
}

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

ruchim

cwlVersion: v1.0
class: Workflow

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

inputs: []

requirements:
  - class: DockerRequirement

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

## 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 = "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

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

ruchim

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

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")