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nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
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Docs: preseq `preseq_step_size` parameter text is misleading. #835

Closed TCLamnidis closed 2 years ago

TCLamnidis commented 2 years ago

Description of the issue

The helptext for --preseq_step_size reads:

Can be used to configure the step size of Preseq's c_curve method. Can be useful when only few and thus shallow sequencing results are used for extrapolation.

Modifies preseq c_curve parameter: -s

Looking into the code (showing only a couple of the cases here, but the option is given in all):

    preseq c_curve -s ${params.preseq_step_size} -o ${input.baseName}.preseq -B ${input} ${pe_mode}
    preseq lc_extrap -s ${params.preseq_step_size} -o ${input.baseName}.preseq -H ${input} -n ${params.preseq_bootstrap} -e ${params.preseq_maxextrap} -cval ${params.preseq_cval} -x ${params.preseq_terms}

The parameter actually modifies -c in both c_curve AND lc_extrap modes, not just the former.

Expected behaviour

Parameter description should be clear that the step size applies to both preseq methods.