This actually looks like you have the opposite ends of corrugated roofing sheets - of different profiles - sitting on top of each other, meeting at the wall in the middle? If so, you would need one row of profiled foam filler to fit the bottom sheet, then sit a different profiled row of foam filler on top of that to fit the profile of the clear sheet.
The lazy option (if you don't care how it looks) is to spray a thin line of expanding foam in there, but be careful as it's easy to spray too much and severely distort the roofing sheets.
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