Specifying output directory

[callumjethomas]

Description of problem

Is it possible to include the option to specify output directory rather than just name?

At the moment when I include a directory path in the -o output option it seems to strip the path, for example:

./scripts/R/pafCoordsDotPlotly.R \
-i ./results/minimap2/ROS3975_hap1_vs_reference.paf.gz \
-o ./results/dotplots/ROS3975_hap1_vs_reference.plot \
-m 2000 -q 500000 -k 7 -s -t -l -p 12

saves the files in the current working directory, rather than in ./results/dotplots/. Is this intended behaviour?

Output

PARAMETERS:
input (-i): ./results/minimap2/ROS3975_hap1_vs_reference.paf.gz
output (-o): ./results/dotplots/ROS3975_hap1_vs_reference.plot
minimum query aggregate alignment length (-q): 5e+05
minimum alignment length (-m): 2000
plot size (-p): 12
show horizontal lines (-l): TRUE
number of reference chromosomes to keep (-k): 7
show % identity (-s): TRUE
show % identity for on-target alignments only (-t): TRUE
produce interactive plot (-x): TRUE
reference IDs to keep (-r):

Number of alignments: 23014
Number of query sequences: 173

After filtering... Number of alignments: 10476
After filtering... Number of query sequences: 40

Version information

R version: 4.5.2
optparse: 1.7.5
ggplot2: 4.0.2
plotly: 4.12.0