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step-by-step pipeline separator conflict #24

@SAMtoBAM

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@SAMtoBAM

Hi there

In the step-by-step pipeline there are several lines that use grep -v '#' to get rid of some headers/notes in certain files
I think this can be changed to grep -v ^'#' to avoid conflicts with '#' separators used in contigs (recommended for PanSN-spec naming) and still removing all comments etc

Cheers

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