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--resume option breaks for custom outfile names #11

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@mhuen

When the names of the outfiles get modified within the scripts for each step (e.g. if the naming pattern differs from the config file), the --resume option will break, since it searches for files with the naming pattern given in the config file.

A clean solution might be to not touch the naming pattern in the scripts and instead to provide more options within the config file.

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