Consistent argument ordering

gitter-lab / SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data

MIT License

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Consistent argument ordering #40

Closed agitter closed 4 years ago

agitter commented 4 years ago

Before we create a standalone SINGE aggregate script for #6, we should standardize the order of the arguments to these scripts:

standalone_SINGE.sh Data gene_list outdir hyperparameter_file runtime_dir
run_SINGE_GLG_Test.sh $runtime $data --outdir $outdir $arg
run_SINGE_Aggregate.sh $runtime $gene_list $data $outdir

SINGE_Aggregate expects the arguments in a different order than the others. Swapping $gene_list and $data would correct this.

agitter commented 4 years ago

We decided to make a single singe.sh script that can run in standalone, GLG, or aggregate modes. The argument order will be: singe.sh runtime_dir GLG data outdir hyperparameter_file 123

With the runtime first, then the mode, then the mode-specific required arguments.