Many of my Qiime2 tools are failing in Galaxy because the wrapper outputs additional html files to $output.files_path, however ‘files_path’ is showing that it is the current job directory Ex: ‘database/job_directory/000/’. The issue seems to be that the files are getting saved to the job directory but $output points to the directory 'database/files/’ directory Ex: database/files/dataset123.dat.
From all of the support I’ve seen online nobody else has had this problem is there a way around this? or at-least to get the directory of the output file without the name of the file?
Here is a snippet of the code I am referring to, Thank you!
qiime tools export --input-path input.qzv --output-path out && mkdir -p ‘$output.files_path’
&& cp -r out/* ‘$output.files_path’
&& mv ‘$output.files_path/index.html’ ‘$output’