All files are required at all stages

[aszabo08]

Hi,

When using gemBS4 seemingly all files are required to perform the subsequent steps (e.g. I receive an error regarding the missing fastq files for the calling and extracting stages when not provided in the pipeline), although this was not needed for gembs3.
This makes the pipeline more complicated compared to the earlier version and was wondering if maybe this could be addressed?

Many thanks,
Anita