Panaroo 1.8.0+galaxy0 fails on GFF3 collection with FileNotFoundError: input_directory/*.gff

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1

Hello,

I encountered what appears to be a wrapper issue in Panaroo (Galaxy wrapper version 1.8.0+galaxy0 on usegalaxy.eu).

Input:

- Collection of 19 GFF3 files

- All files were generated by Bakta

- Collection datatype: gff3

The job fails immediately with:

FileNotFoundError: [Errno 2] No such file or directory: ‘input_directory/*.gff’

Relevant traceback:

Traceback (most recent call last):

File “/usr/local/bin/panaroo”, line 10, in

sys.exit(main())

File “/usr/local/lib/python3.11/site-packages/panaroo/_main_.py”, line 318, in main

with open(args.input_files[0], “r”) as file:

FileNotFoundError: [Errno 2] No such file or directory: ‘input_directory/*.gff’

From the generated command line I can see that the wrapper creates symlinks such as:

input_directory/SRR38521030_Staphylococcus_aureus_ST8_CC8

(without .gff extension)

but Panaroo is invoked with:

-i input_directory/*.gff

This suggests that no files match the wildcard and Panaroo receives the literal string ‘input_directory/*.gff’.

Could this be a wrapper issue related to handling GFF3 collections?

Thank you.

2

Hello @Loc_Le

Yes, this tool is a bit tricky to use. A full adjustment at the tool wrapper level is pending but for now, the solution is to include .gff on the collection identifiers.

You can recreate the collection (retaining the file extensions) or use the Extract Element identifiers, text editing tools, then Relabel identifiers functions to add these back in. And, for HTP use cases, Apply Rules can make this sort of adjustment too.

Recreating the collection is the easiest, so try that first if this seems overly complicated.

Hope this helps and follow up questions are welcome! :slight_smile: