utility-wdls

Short workflows to run common tasks.

make-fofn

Purpose :

Creates a text file listing the file paths provided as input.

Requirements/expectations :

• An array of file paths.

Output :

• A file containing a list of file paths.

generate-sample-map

Purpose:

Generate a sample_map file, which can be used for JointGenotyping workflow.

Requirements/expectations :

• An array of file paths
• An array of file names
• Name of output sample_map

Outputs :

• sample map file

copy-files-to-directory

Purpose:

This workflow copies an array of files from a gs bucket to another specfied gs bucket

Requirements/expectations :

• Array[String] files_2_copy = Files to copy
• String output_gs_dir = Directory to copy files to

Outputs :

• File output_text_file = The bash script used to copy files
• Array[String] new_file_paths = Files contained in the output bucket

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Software version notes :

• Cromwell version support
  • Successfully tested on v53

Important Notes :

• Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
• The provided JSON is a generic ready to use example template for the workflow. It is the user’s responsibility to correctly set the reference and resource variables for their own particular test case using the GATK Tool and Tutorial Documentations.
• For help running workflows on the Google Cloud Platform or locally, please view the following tutorial (How to) Execute Workflows from the gatk-workflows Git Organization.
• Relevant reference and resources bundles can be accessed in Resource Bundle.

Contact Us :

• The following material is provided by the Data Sciences Platform group at the Broad Institute. Please direct any questions or concerns to one of our forum sites : GATK or Terra.

LICENSING :

Copyright Broad Institute, 2019 | BSD-3

This script is released under the WDL open source code license (BSD-3). 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.