Example of the internals of a cromwell script (taken from the GenotypeGVCFs task of the GATK4 pipeline_)

cromwell-script.sh

#!/bin/bash

cd /cromwell_root
tmpDir=$(mkdir -p "/cromwell_root/tmp.b3852e07" && echo "/cromwell_root/tmp.b3852e07")
chmod 777 "$tmpDir"
export _JAVA_OPTIONS=-Djava.io.tmpdir="$tmpDir"
export TMPDIR="$tmpDir"
export HOME="$HOME"
(
cd /cromwell_root
touch /cromwell_root/monitoring.log
chmod u+x /cromwell_root/monitoring.sh
/cromwell_root/monitoring.sh > /cromwell_root/monitoring.log &
)
(
cd /cromwell_root


set -e

tar -xf /cromwell_root/wustl-ccdg-costa-rican-callset-2018-11/cromwell/cromwell-executions/JointGenotyping/94b704be-7057-4eda-9622-28cd51749cfd/call-ImportGVCFs/shard-8204/genomicsdb.tar
WORKSPACE=$( basename /cromwell_root/wustl-ccdg-costa-rican-callset-2018-11/cromwell/cromwell-executions/JointGenotyping/94b704be-7057-4eda-9622-28cd51749cfd/call-ImportGVCFs/shard-8204/genomicsdb.tar .tar)

/gatk/gatk --java-options "-Xmx5g -Xms5g" \
 GenotypeGVCFs \
 -R /cromwell_root/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta \
 -O output.vcf.gz \
 -D gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf \
 -G StandardAnnotation \
 --only-output-calls-starting-in-intervals \
 --use-new-qual-calculator \
 -V gendb://$WORKSPACE \
 -L chr16:33757666-34097266
)  > '/cromwell_root/stdout' 2> '/cromwell_root/stderr'
echo $? > /cromwell_root/rc.tmp
(
# add a .file in every empty directory to facilitate directory delocalization on the cloud
cd /cromwell_root
find . -type d -empty -print0 | xargs -0 -I % touch %/.file
)
(
cd /cromwell_root
sync


)
mv /cromwell_root/rc.tmp /cromwell_root/rc

GenotypeGVCF.wdl

task GenotypeGVCFs {
  File workspace_tar
  String interval

  String output_vcf_filename

  String gatk_path

  File ref_fasta
  File ref_fasta_index
  File ref_dict

  String dbsnp_vcf
  String docker
  Int disk_size

  command <<<
    set -e

    tar -xf ${workspace_tar}
    WORKSPACE=$( basename ${workspace_tar} .tar)

    ${gatk_path} --java-options "-Xmx5g -Xms5g" \
     GenotypeGVCFs \
     -R ${ref_fasta} \
     -O ${output_vcf_filename} \
     -D ${dbsnp_vcf} \
     -G StandardAnnotation \
     --only-output-calls-starting-in-intervals \
     --use-new-qual-calculator \
     -V gendb://$WORKSPACE \
     -L ${interval}
  >>>
  runtime {
    docker: docker
    memory: "7 GB"
    cpu: "2"
    disks: "local-disk " + disk_size + " HDD"
    preemptible: 5
  }
  output {
    File output_vcf = "${output_vcf_filename}"
    File output_vcf_index = "${output_vcf_filename}.tbi"
  }
}