Questions tagged [wdl]

Workflow Description Language; used to specify data processing and analysis workflows with a human-readable and -writeable syntax.

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How do I force Cromwell / WDL to put input files in the same directory?

I have a cromwell task that, among other variables, takes these three variables: ...
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1answer
33 views

What changed wwith Python in WDL change from draft 2 to version 1?

I'm updating my WDL from draft 2 (whichs works fine) to version 1. I'm stuck with a Py snippet ...
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1answer
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How do I rename output folder created using WDL's glob function, with cromwell execution engine?

I made a wdl (genomics pipeline language by the Broad Institute) task for fastqc that outputs the zip files, of which there will be as many as reads that the sample I'm working on at that moment has. ...
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29 views

Reading nested Map data structures in WDL

I'm having trouble getting WDL's read_json to work as expected when trying to create a Map[String, Map[String, String]] data ...
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1answer
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Pointing Cromwell to local EBS mounted storage on AWS Batch

I'm trying to run the WDL tasks from the GTEx RNA-Seq pipeline with Cromwell using AWS Batch as a backend. I store the STAR alignment index on an Elastic Block Store since my Cromwell server instance ...
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How do I get cromwell to create soft-links?

The file system I'm running on doesn't allow the creation of hard-links. Cromwell is trying to create hard-links to directories, and when that fails, it's copying them. Which is leading to disk ...
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2answers
72 views

Scatter tasks around predefined batches inside a WDL workflow

Suppose I have two arrays Array[File] X and Array[String] Y both of length N, with Y being a sort of R-like factor that defines batch membership for X, for a total of M batches with M < N. A valid ...
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1answer
110 views

output Array[Pair[X,Y]] to file inside a WDL task

If I zip two arrays I obtain an Array[Pair[String,String]] variable. Now if I want to output to file an Array[Array[String]] I can use write_tsv(), if I want to output to file a Map[String,String] I ...
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1answer
88 views

Matching files by chromosome during wdl scatter gather

I'm trying to implement a polygenic score pipeline in WDL and I'm quite new to this pipeline management. The first step of the pipeline takes a file of GWAS summary statistics and splits it by ...
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1answer
114 views

How to generate the json files for Cromwell workflow execution?

I am starting to use Cromwell WDL scripts for running GATK workflows on a slurm cluster. When using the paired-fastq-to-unmapped-bam script I need to define the fastq sepcifics in the appropriate json ...
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243 views

Using Broad Institute RNAseq pipeline

There is a Github report 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 ...