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Multiple modifications calling #46

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HudoGriz
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Hello,

After discussing the issues related to multiple modifications calling within wf-basecalling with Angelica Vittori, I am opening this pull request to suggest a feature enhancement based on our solution.

Problem

Currently, wf-basecalling only accepts a single string argument for the remora_cfg parameter. This limits the ability to utilise multiple model references, which is a feature supported by dorado. For example: dorado basecaller hac,5mC_5hmC,6mA path/to/pod5 > calls.bam.

Solution

I have implemented minimal changes to allow wf-basecalling to accept an array of multiple model names via the -params-file.

Kind regards,

Blaž

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