How-to Guide: Capturing stdout with CWL¶

This guide explains how to capture the standard output (stdout) of a CommandLineTool in CWL.

The example focuses on the stdout and outputs blocks to save the tool's output to a file and make it available for further use.

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cwl_file=../cwl-workflows/return-output-file.cwl

cat $cwl_file | yq e .'$graph[1]' | yq '.. | select(has("outputs")) | {"outputs": .outputs}' 
cwl_file=../cwl-workflows/return-output-file.cwl

cat $cwl_file | yq e .'$graph[1]' | yq '.. | select(has("outputs")) | {"outputs": .outputs}'

This block ensures the tool captures and returns the preview.png file generated during execution.

Objective¶

Convert a Sentinel-2 GeoTIFF file into a PNG image.

Capture the generated PNG file as the tool's output using the outputs block.

Steps¶

Understand the outputs Block

In CWL, the outputs block specifies:

Name: preview – the logical name of the output.
Type: File – indicates the output is a file.
outputBinding.glob: Specifies the file's name or pattern to locate the file in the tool's working directory.

From the example:

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cat $cwl_file | yq e .'$graph[1]' | yq '.. | select(has("outputs")) | {"outputs": .outputs}' 
cat $cwl_file | yq e .'$graph[1]' | yq '.. | select(has("outputs")) | {"outputs": .outputs}'

glob: preview.png: Ensures the tool captures the file preview.png generated by the rio convert command.

Review the return-output-file.cwl Workflow

The workflow (return-output-file.cwl) is defined as:

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yq -e . $cwl_file
yq -e . $cwl_file

It's graphical representation:

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cwltool --print-dot $cwl_file 2> /dev/null | dot -Tpng | display
cwltool --print-dot $cwl_file 2> /dev/null | dot -Tpng | display

Provide Input Parameters

Create an input file inputs.yml with the GeoTIFF URL:

tif: "https://sentinel-cogs.s3.us-west-2.amazonaws.com/sentinel-s2-l2a-cogs/10/T/FK/2021/7/S2B_10TFK_20210713_0_L2A/TCI.tif"

Execute the Workflow

Run the workflow using cwltool:

cwltool return-output-file input.yml

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cat > input.json <<'JSON'
{
  "tif": {
    "value": "https://sentinel-cogs.s3.us-west-2.amazonaws.com/sentinel-s2-l2a-cogs/10/T/FK/2021/7/S2B_10TFK_20210713_0_L2A/TCI.tif"
  }
}
JSON
cwltool --podman "$cwl_file" input.json > output.json
cat > input.json <<'JSON'
{
  "tif": {
    "value": "https://sentinel-cogs.s3.us-west-2.amazonaws.com/sentinel-s2-l2a-cogs/10/T/FK/2021/7/S2B_10TFK_20210713_0_L2A/TCI.tif"
  }
}
JSON
cwltool --podman "$cwl_file" input.json > output.json

Expected Output¶

The rio tool processes the input GeoTIFF and generates a PNG file named preview.png.

The outputs block ensures:

The file is located using glob: preview.png.
It is made available as the workflow output.

Example Workflow Output:

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cat output.json | yq e . - 
cat output.json | yq e . -

The preview.png file is now accessible in the working directory or as defined by the CWL runner.

Key Takeaways¶

The outputs block defines how to capture and return files:
- type: File: Specifies the output type.
- outputBinding.glob: Matches the file name or pattern.
Ensure the file name in glob matches the file name generated by the tool (preview.png).

By focusing on the outputs block, this guide highlights how to capture and return output files in CWL workflows.

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rm -f output.json
rm -f input.yml
rm -f preview.png
rm -f output.json
rm -f input.yml
rm -f preview.png