Failure to assign replicates

[arisp99]

Bug Description

Following the fixes in #22 where the sample sheet preparation was updated, I have been unable to generate a sample sheet without running into errors. Namely, the error occurs when the script attempts to assign a replicate number to each grouped sample and sample set here:

MIPTools/src/sample_sheet_prep.py

Lines 133 to 135 in 8e3ed00

	sample_sheet["Replicate"] = sample_sheet.groupby(
	["sample_name", "sample_set"])["replicate"].transform(
	assign_replicate).astype(int)

Digging into the code a bit more, the new replicate column is filled with NaN. Somehow, the assign_replicate function is generating NaN instead of the true replicate number. This causes the astype(int) command to fail as it cannot coerse NaN into an integer.

Steps to Reproduce

1. Build or download the development version of the container.
2. Isolate a capture plate and sample plate from a sequencing run.
3. Run:

   $ singularity exec -B /work/apascha1/sample-sheet-prep:/opt/analysis \
     $miptools_dev.sif python /opt/src/sample_sheet_prep.py \
     --capture-plates capture_plates.tsv --sample-plates sample_plates.tsv --output-file samples.tsv

This should raise the following exception:

Exception: Error in assigning replicates. Please make sure the 'sample_name' and 'sample_set' fields have valid, non-empty values in all provided files.

Expected Behavior

There should be no NaNs in the replicate column after assigning replicates.

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@aydemiro Do you have any idea what might be going wrong in the assign_replicate function?