CNVkit batch module went through an uncontrolled pandas upgrade which makes it crash

[priesgo]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

When using the module cnvkit/batch with conda the following error is raised:

ImportError: cannot import name 'Int64Index' from 'pandas'

I found that the version 0.9.9 from May 2021 of cnvkit is defined in this line https://github.com/nf-core/modules/blob/master/modules/nf-core/cnvkit/batch/main.nf#L5, but the pandas version in the dependency tree is not controlled, thus as of today latest pandas 2.0.2 gets installed which is incompatible and raises the error above.

An upgrade to cnvkit 0.9.10 seems to fix the issue.

Command used and terminal output

I used this module programmatically.

Relevant files

No response

System information

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