Cromwell WDL experiments

Requirements

The fetcher scripts require curl, except for the Broad 0/fetch_data.sh scripts which require wget

Java 8 (and possibly NOT 9 or 10)

Install

Download Cromwell and WOMtool JARs

0/fetch_jars.sh
0/fetch_gatk.sh

Download the above plus all data files for Broad tutorials

0/fetch_all.sh

Cleanup

Remove all generated output files in all directories

0/clean_all_outputs.sh

Remove all downloaded data (by 0/fetch_data.sh)

0/clean_all_data.sh

Remove all downloaded files

0/clean_all_downloaded.sh

Run all of the above

0/clean_all.sh

Usage (all)

The location of the Cromwell and WOMtool JARs is specified by

CHAMBER_0005_CROMWELL_JAR
CHAMBER_0005_WOMTOOL_JAR

and can be appropriately set to the JARs downloaded by 0/fetch_jars.sh

. 0/env.sh

in the root of this repository. Most of the per-experiment scripts rely on this variable being set.

Simple local experiments

All of these can be validated and run

cd DIRECTORY
./0/validate.sh
./0/run.sh

hello         Basic example with simple input

MGI LSF experiments

Simple experiments running scatter and serial tasks with the MGI cluster as backend

MGI_LSF/
  simpleLSF     Three serial tasks
  scatterLSF    Three scatter tasks followed by two serial tasks
  dockerLSF     As in "simpleLSF" but with a docker container specified
                for each task

Modified local Broad tutorials

The directories

Broad/
  helloHaplotypeCaller
  simpleVariantSelection
  simpleVariantDiscovery
  jointCallingGenotypes

contain files modified from four of the tutorials at

https://software.broadinstitute.org/wdl/documentation/topic?name=wdl-tutorials

All of them are designed to use the Cromwell, WOMtool, and GATK files downloaded in the Install section, as well as downloaded data and modified versions of the tutorial files that work with GATK 4.x. To run each do eg

cd helloHaplotypeCaller

# If 0/fetch_all.sh was not run, download the data files
0/fetch_data.sh

# Run Cromwell
0/run.sh

# To clean up Cromwell output directories
0/clean_outputs.sh

Credits

helloHaplotypeCaller
simpleVariantSelection
simpleVariantDiscovery
jointCallingGenotypes

are all modified from the original Broad tutorial examples at

https://software.broadinstitute.org/wdl/documentation/topic?name=wdl-tutorials

See the README under each for links