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NorwegianVeterinaryInstitute / DemultiplexRawSequenceData

A workflow automation script: demultiplex the library sequence, run quality checks, deliver to archiving and processing afterwards
GNU General Public License v3.0
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bug: Some software save values quoted and prevent the code of getting the index of demux.Sample_Sheet #67

Closed georgemarselis-nvi closed 1 year ago

georgemarselis-nvi commented 1 year ago

Copying ticket over from https://github.com/NorwegianVeterinaryInstitute/nvi_lims_epps/issues/28

I edited the relevant SampleSheet twice: once at work and then in the evening at home.

In libreoffice and excel everything looks just fine:

image

as text, though, the file at work looks like this (after saving) image

every field is quoted!

therefore, the code is not comparing for 'Sample_Project', but for '"Sample_Project"'! the quotes are part of the string token!

Solution:

  1. preliminary strip any single or double quotes from the current processing line
  2. Complain loudly if a single quote or double quote is found.

@magnulei what are the chances this part of the data will have quotes in the values?

image

georgemarselis-nvi commented 1 year ago

it is fixed on the new demultiplexing script but i will also add it to the old one ,just in case.

as soon as magnus replies i'll close the ticket.

magnulei commented 1 year ago

I would say that the probability of this happening to a sample sheet produced by clarity is close to zero. Cant say for sure though as I havent seen the code that produce the sample sheet. Its inside Illuminas groovy tar script archive.

But of course if somebody opens the file to make some modifications then it could happen again I guess. So good to catch it in the script.

I am happy :)

georgemarselis-nvi commented 1 year ago

awesome. I will close the ticket, then.