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sanctuuary / APE

APE (Automated Pipeline Explorer)
https://ape-framework.readthedocs.io
Apache License 2.0
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[BUG] CWL workflows and graphs not generated unless number_of_generated_graphs is set to 0 #113

Closed Ambivalentalfa closed 2 months ago

Ambivalentalfa commented 3 months ago

Note: Not all fields are obligatory, but the more details you provide, the easier it will be for us to address the issue. Feel free to omit sections that you feel are not relevant to your report.

Description

Running APE on Linux doesn't generate CWL workflows or graphs as expected. The terminal output looks correct, but only an empty Figures directory and a solutions.txt file (no CWL directory) are created.

API/CLI Version

APE Version

2.3.0

Java Version

17.0.10

Steps to Reproduce

  1. Run APE with number_of_generated_graphs: "10" and "number_of_cwl_files": "10"
  2. Check output directory if CWL files created

Expected Behavior

Getting figures in the Figures directory, and a CWL directory with CWL workflows.

Actual Behavior

Only an empty Figures directory and a solutions.txt were created. No CWL directory. Picture includes one run with "debug_mode": "true" (top) and one run with "debug_mode": "false" (bottom). APE_debug_terminal_out

Possible Solution

Setting number_of_generated_graphs to "0" solves the issue temporarily.

Additional Context

Ambivalentalfa commented 2 months ago

Reinstalling graphviz solved the problem!