Issue in normalization about simpli HOT 5 CLOSED

Works perfectly, thank you so much!

from simpli.

Hi,

I am not sure why you are getting these lines in the terminal output:

sample (printed from: main.nf) : sample_1
sample (printed from: workflow normalize_images) : sample_1
sample (printed from: main.nf) : sample_2
sample (printed from: workflow nor
[tiff_input_metadata.csv](https://github.com/ciccalab/SIMPLI/files/8777945/tiff_input_metadata.csv)
malize_images) : sample_2
sample (printed from: process normalize_tiffs): sample_1

Did you add the some extra code or options for printing?
Anyway, I think your sample_metadata.csv file is OK but your tiff_input_metadata.csv has a small issue. It is not expected for samples to have different markers and labels could you retry with this attached version?

tiff_input_metadata.csv

If this does not help could you send me your nextflow log file for the run to invesstigate further?

Best,

Michele

from simpli.

Thanks for your help, but the metadata file you provided didn't solve the issue. It still normalizes only the first sample. Here is my nextflow.log file:

nextflow.log

And about the terminal output, yes I added some extra printing to better understand where the problem might be.

Thanks!

from simpli.

OK, it was due to a small bug which should be now fixed.
Please see this commit for details: 34b48fa

Could you give it a go and let me know if you have any issues.
Thank you for reporting this.

from simpli.

No problem at all, thank you for reporting this issue.

from simpli.