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External Argument Documentation #1313
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The desired top-level documentation is available on the nf-core website, but not duplicated for each pipeline. RSEM does not allow passing custom arguments to STAR, so there is nothing that can be done there. Regarding the |
Hi @MatthiasZepper , thanks for the reply. Yes, I saw the info on the nf-core website for |
There is no priority or level. Using In about 1% of the modules, a second set of arguments is needed, e.g. because they are positional arguments or because the module comprises a second tool that requires
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Description of feature
Given that the modules.config file contains the following:
It would be very helpful to have some top level documentation to explain how to pass those arguments into their respective programs. For example, when discussing SortMeRNA, it would be nice to have some direction on how to pass arguments like:
--no-best
or--idx-dir
to it via those variables. The same is true for STAR, which offers additional options when combined with Salmon, but not RSEM. While program defaults often work, they are not ideal, and the ability to configure a pipeline at the top level seems better than making changes deep down in the module config files.
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