Friederike Hanssen

Yes, currently it is only possible to do one "type" of pre-processing. I would transfer this to a bigger feature requests: For scenarios such as above, it would be nice...

Other current options as a work around: Utilize the `--step` functions to run the one tool that needs different preprocessing on the respective `csv` file that is available in `results/csv`...

Thank you for reporting! will look into a fix

Commenting to upvote this issue, facing the same thing at the moment :)

Hey! Let's keep this open until it is actually merged into the pipeline and added to the changelog or we will forget :)

Hi @Raghu9721 ! Sorry just saw this, I am not the pyTMB tool developer. I would ask here to get help from them for this: https://github.com/bioinfo-pf-curie/TMB

On a good way with this new beautiful documentation #981

I am unsure whether it actually makes sense to provide these files. Do all manufucatures use the same coordinates in their kits? Otherwise I think we should rather aim for...

@asp8200 How is this handeled currently? Is this issue still relevant?

added in #470 , also cleaned up the `-profile cfc` docs