run_autogvp.sh allows the user to define an outdir but 04-filter_gene_annotations.R sets the outdir to root.dir/results. If the user defines a different outdir, 04-filter_gene_annotations.R fails. Can we either remove the outdir flag from run_autogvp.sh or set the outdir to the user defined one in 04-filter_gene_annotations.R?
run_autogvp.sh allows the user to define an outdir but 04-filter_gene_annotations.R sets the outdir to root.dir/results. If the user defines a different outdir, 04-filter_gene_annotations.R fails. Can we either remove the outdir flag from run_autogvp.sh or set the outdir to the user defined one in 04-filter_gene_annotations.R?