Running shelley-bio-batch with multiple tools causes a crash during table rendering via rich.
The tool starts correctly and displays the header UI, but fails when attempting to render the tools table. I have no current workaround.
Traceback (most recent call last):
File "/usr/local/bin/shelley-bio-batch", line 7, in <module>
exec(compile(f.read(), __file__, 'exec'))
File "/opt/shelley-bio/bin/shelley-bio-batch", line 16, in <module>
main()
File "/opt/shelley-bio/shelley_bio/scripts/batch_builder.py", line 160, in main
sys.exit(batch_build_modules(tools))
File "/opt/shelley-bio/shelley_bio/scripts/batch_builder.py", line 94, in batch_build_modules
console.print(tools_table)
File "/usr/local/lib/python3.10/dist-packages/rich/console.py", line 1724, in print
extend(render(renderable, render_options))
File "/usr/local/lib/python3.10/dist-packages/rich/console.py", line 1345, in render
for render_output in iter_render:
File "/usr/local/lib/python3.10/dist-packages/rich/table.py", line 515, in __rich_console__
yield from self._render(console, render_options, widths)
File "/usr/local/lib/python3.10/dist-packages/rich/table.py", line 768, in _render
self.box.substitute(
AttributeError: 'str' object has no attribute 'substitute'
Description
Running shelley-bio-batch with multiple tools causes a crash during table rendering via rich.
The tool starts correctly and displays the header UI, but fails when attempting to render the tools table. I have no current workaround.
Command tested:
shelley-bio-batch samtools fastqc bowtie2Expected Behavior
but It crashes with the following traceback: