Overview

Teaching: 20 min
Exercises: 10 min

Questions

• What kind of custom logic can happen between steps?

Objectives

• Customize the STAR output filename to use the input filename.

• Organize files into directories.

Expressions on step inputs

You might have noticed that the output bam files are all named Aligned.sortedByCoord.out.bam. This happens because because when we call STAR, it gives the output a default file name.

During workflow execution, this is usually not a problem. The workflow runner is smart enough to know that these files are different and keep them separate. This can even make development easier by not having to worry about assigning unique file names to every file. Also, if we intend to discard the BAM files as intermediate results

However, it is a problem for humans interpreting the output. We can fix this by setting the parameter OutFileNamePrefix on STAR. We want the output filename to be based on the input filename.

In alignment.cwl, we can use valueFrom on the OutFileNamePrefix input parameter to construct the output prefix from the input filename.

requirements:
  StepInputExpressionRequirement: {}

steps:
  ...
  STAR:
    ...
    in:
      ForwardReads: fq
      ...
      OutFileNamePrefix: {valueFrom: "$(inputs.ForwardReads.nameroot)."}

The code between $(...) is called an “expression”. It is evaluated when setting up the step to run, and the expression is replaced by the result to get the parameter value.

An expression can refer to other inputs to the step that are either directly connected to another value, or have a default value. Here, we refer to the input parameter ForwardReads, which is our fastq input file.

ForwardReads is a File object, not a plain file name, so it has some fields of its own. The file object has a number of fields that we can use. These include basename (the name of the file, without a directory), size (file size, in bytes), nameext (the last file extension) and nameroot (the name with nameext removed). Using

Finally, our expression is embedded in a string, so after replacing the expression with the value of inputs.ForwardReads.nameroot, it adds the remainder of the string, which just is a dot .. This is to separate the leading part of our filename from the “Aligned.bam” extension that will be added by STAR.

Organizing output files into Directories

You probably noticed that all the output files appear in the same directory. You might prefer that each file appears in its own directory. This will show you how to do that.

Unlike shell scripts, in CWL you cannot call mkdir and mv to organize files into directories. This is because the output files, at this point, do not actually exist together in one directory. They may exist on different nodes, in different directories, or different cloud buckets. In CWL, instead of moving files around directly, you tell the runner you want your directory to look like, and it will create it for you.

We can use an “expression” to create a Directory object describing each of our directories. An expression is a piece of Javascript code which is executed by the workflow runner to produce values that affect the workflow. These can be a simple as substituting the value of an input variable, or as complex as en entire function that generates new objects.

Javscript code must be bracketed inside $(...) or ${...}. The difference comes down to syntax. The $() form is more compact but can only include code that can appear on the right side of an assignment (=), which cannot include control blocks like if or for. The ${} form is a Javascript function, which can include control blocks, and must end in a return statement.

Expressions can both appear in valueFrom fields as well as some other fields, or in an ExpressionTool which, like Workflow or CommandLineTool has explicitly defined inputs and outputs sections.

The approach here is to define an expression tool which takes a

The Directory object has two fields, basename and listing. The basename is the name of the directory, and the listing is the contents, which consists of other File and Directory objects.

Create subdirs.cwl:

cwlVersion: v1.2
class: ExpressionTool
requirements:
  InlineJavascriptRequirement: {}
inputs:
  fq: File[]
  bams: File[]
  qc: File[]
outputs:
  dirs: Directory[]
expression: |-
  ${
  var dirs = [];
  for (var i = 0; i < inputs.bams.length; i++) {
    dirs.push({
      "class": "Directory",
      "basename": inputs.fq[i].nameroot,
      "listing": [inputs.bams[i], inputs.qc[i]]
    });
  }
  return {"dirs": dirs};
  }

Then change main.cwl:

steps:
  ...
  output-subdirs:
    run: subdirs.cwl
    in:
      fq: fq
      bams: alignment/bam_sorted_indexed
      qc: alignment/qc_html
    out: [dirs]
outputs:
  dirs:
    type: Directory[]
    outputSource: output-subdirs/dirs
  featurecounts:
    type: File
    outputSource: featureCounts/featurecounts

Running the workflow

Run the workflow. Look at the output. The BAM and fastqc files should now be organized into directories, with better naming of the bam files.

Episode solution

• main.cwl
• alignment.cwl
• featureCounts.cwl
• subdirs.cwl

Key Points

• CWL expressions allow you to use custom logic to determine input parameter values.

• CWL ExpressionTool can be used to reshape data, such as declaring directories that should contain output files.