Semibin2: working files cannot be found if they start with ‘.’ (filenames inherited from input files)

[cat-bro]

We’ve had some jobs fail on Galaxy Australia because the name of the bam file in the working directory is “.fastqsanger.bam” which is inherited from the input file name “.fastqsanger” and the job fails with "Error: Expected file '*.bam' does not exist” and I think it just can’t find it because it starts with a “.” and is therefore hidden.

the working bam file name is set here: https://github.com/galaxyproject/tools-iuc/blob/main/tools/semibin/macros.xml#L161-L162

This is similar but not the same as issue #7326

[SantaMcCloud]

I will change this in the new version of the wrapper since therer is an update to 2.2.0 or should it be first getting fix in the current version and then have the update comming?

[SantaMcCloud]

#7366