CODEWITHSUNDEEP
pythonsnakemake
lalligagger
lalligagger

Reputation: 51

Can external scripts be included in Snakemake report?

Similar to the following questions, I could not find a definite answer to whether or not external scripts (e.g. .py source) can be included in report as code blocks under the rule table.

Do reports only display code that's inline within the Snakefile? Is there a way to include external scripts?

It's a great framework as far as I've been able to explore it!

Include Parameters and source code in Snakemake HTML Report

Snakemake report - Code not displayed in the report

Upvotes: 2

Views: 206

Answers (1)

SultanOrazbayev
SultanOrazbayev

Reputation: 16571

This appears to be a bug that appeared sometime after version 6.4.1, I provide a minimal reproducible example in the relevant GH issue.

One option right now is to install the old version before generating the report:

pip install snakemake==6.4.1
snakemake --report
# can revert back to the latest version
# pip install -U snakemake

The generated report will include code blocks for the included scripts. This is not ideal, but should work until the bug is fixed.

Upvotes: 2

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