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merge specific params #144

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tiagofilipe12 opened this issue Oct 9, 2018 · 0 comments
Open

merge specific params #144

tiagofilipe12 opened this issue Oct 9, 2018 · 0 comments
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discussion enhancement New feature or request

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@tiagofilipe12
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At the moment --merge_params argument allow us to merge all the parameters that are repeated through the pipeline, while not providing this option will make a unique parameter for each component. However there will be some cases where the user will want to set a given parameter global to the entire pipeline (e.g. genomeSize). For that it would be cool if when this parameter is passed we could provide a list of all the parameters that we want to merge.

flowcraft.py build -t "trimmomatic (spades | skesa)" -o outputfile.nf --merge_params "genomeSize, minCoverage"

If we want to merge all the parameters it could be just like it is at the moment but if a string is provided after the parameter then it should take only those parameters to merge them.
So, the default behavior would remain the same, i.e., if no --merge_params is given there won't be any merging, if --merge_params is provided without anything else it would merge all the parameters in a given pipeline. But if a string with a list of parameters separated by commas is provided then it would only merge those parameters throughout the pipeline and all the other ones would remain with the param_idexclusive of each process.

@tiagofilipe12 tiagofilipe12 added the enhancement New feature or request label Oct 9, 2018
@tiagofilipe12 tiagofilipe12 changed the title merge params for specific params merge specific params Oct 9, 2018
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