Answers.Body: <p>You need to follow the <a href="https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/README.md" rel="nofollow noreferrer">readme</a> of this folder to  use the pipeline, there you will find instructions about how to align, mark duplicates, quantificate, and aggregate the results.</p>
  
  <p>If you want to execute the WDL scripts you can follow <a href="https://software.broadinstitute.org/wdl/documentation/execution.php" rel="nofollow noreferrer">this guide</a> using Cromwell. Basically use: <code>java -jar Cromwell.jar run myWorkflow.wdl --inputs myWorkflow_inputs.json</code></p>
  
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Answers.CreationDate: 2018-09-21T07:18:08.260Z
Answers.LastActivityDate: 2018-09-21T07:18:08.260Z
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Body: <p>There is a <a href="https://github.com/broadinstitute/gtex-pipeline/tree/master/rnaseq" rel="nofollow noreferrer">Github report</a> for Broad's pipeline on RNA-Seq. It has a docker build file and WDL scripts.</p>
  
  <p>However, I don't see how any of the WDL script is being used in the docker (Dockerfile). It looks like Broad's docker runs on the standard command-line tools, but not via the WDL language.
  How do the Broad bioinformaticians take advantage of the WDL scripts?</p>
  
Tags: <rna-seq><docker><wdl>
Title: Using Broad Institute RNAseq pipeline
ThreadText: # Using Broad Institute RNAseq pipeline
  
  (Asked by: username_0 on 2018-09-21)
  
  There is a [Github report](https://github.com/broadinstitute/gtex-pipeline/tree/master/rnaseq) for Broad's pipeline on RNA-Seq. It has a docker build file and WDL scripts.
  
  However, I don't see how any of the WDL script is being used in the docker (Dockerfile). It looks like Broad's docker runs on the standard command-line tools, but not via the WDL language.
  How do the Broad bioinformaticians take advantage of the WDL scripts?
  
  **Tags:** rna-seq, docker, wdl
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-09-21. Score: 2 | Accepted answer
  
  You need to follow the [readme](https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/README.md) of this folder to use the pipeline, there you will find instructions about how to align, mark duplicates, quantificate, and aggregate the results.
  
  If you want to execute the WDL scripts you can follow [this guide](https://software.broadinstitute.org/wdl/documentation/execution.php) using Cromwell. Basically use: `java -jar Cromwell.jar run myWorkflow.wdl --inputs myWorkflow_inputs.json`
  
  
  ---
  
  