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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Error when trying to move multiple file types in wdl

I tried to add a "gather_results" task to a workflow that takes in an array of Files and moves output files to a new folder of a specified name. ...
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1answer
43 views

Extracting WDL map keys as a task

I want to get the array of keys from a map data structure, so I can perform array-based functions against the map in subsequent tasks. I am limited to draft-2 ...
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37 views

Why can't my cromwell job localize input files? It only happens some of the time

Like the title says, my Cromwell jobs can't localize input files consistently. I get a Could not localize error, and then a ...
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13 views

Cromwell - Sending JSON of inputs without the workflow name

In this workflow example: version 1.0 workflow foo { input { Array[Pair[File,File]] fastqFiles } } I would send my inputs as: ...
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25 views

How do I keep a glob from copying a file in Cromwell / WDL

Using Crowell 52. When I do a glob to get matching files, Cromwell places a copy of each matching file in the glob-* directory. As these are multi-gigabyte Bam files, I'd really prefer for Cromwell ...
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1answer
103 views

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
440 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
146 views

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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94 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
60 views

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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61 views

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
195 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
251 views

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

I have a table containing different metadata information about a set of samples as an Array[Object] and I need to extract a couple of columns from this table and output those two columns into a file ...
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154 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
268 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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279 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 ...