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fix: update CI workflow, snakemake wrappers and python / pandas code syntax #40

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Instead, use the .squeeze("columns") function, as for example done here:
https://github.com/sktime/sktime/pull/2693/files

This closes #39, with more relevant info over there.

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dlaehnemann commented Jun 6, 2023

I merged in #41 , as the tests there fail with the failure that this PR fixes. So we should probably merge this all at once.

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This fix exposed a lot of parts of the workflow that haven't aged well, so in addition to updating the CI workflow, I will now also update all the wrappers. And change the name of the pull request accordingly.

@dlaehnemann dlaehnemann changed the title fix: stop using deprecated pd.read_table argument squeeze fix: update CI workflow, snakemake wrappers and python / pandas code syntax Jun 7, 2023
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TypeError in calling.smk rule merge_variants. The bwa mapping stops after creating the indexes files.
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