update meta map guidelines for reference file inputs #1987
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@ramprasadn there are some conflicts. |
cmatKhan
reviewed
Aug 27, 2024
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| 3. All _non-mandatory_ command-line tool _non-file_ arguments MUST be provided as a string via the `$task.ext.args` variable. | ||
| 3. Non-file mandatory arguments or arguments needed to modify the command to make the module run with no error, SHOULD be provided as value channels (for example `lib_type` in [salmon/quant](https://github.com/nf-core/modules/blob/master/modules/nf-core/salmon/quant/main.nf)) - see 'Input/output options' below. |
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I think rather than referring to 'non-file' in the current points 3. and 4. ... It would be better to separate that into its own bullet point. eg,
filearguments, whether or not they are mandatory, should be provided as input channels (for example, thefaiargument in samtools faidx)
I'm torn as to whether that should come before or after the current point 3.
On the one hand, it seems like mandatory arguments are more important, and hence addressed first.
On the other, it is probably a more necessary reminder to include non-mandatory file arguments, which the author themselves may never use, as module input.
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As discussed in the nf-core maintainers meeting, I have updated the guidelines for creating new modules to add a meta map to channel definitions that carry reference file inputs.