Changes conflicting in pull request

[cpavloud]

I propose these changes to the run-information-batch-001.csv, run-information-batch-002.csv, run-information-batch-001_column-descriptions.csv and run-information-batch-002_column-descriptions.csv:

1. The proper name of the parameter in the https://github.com/emo-bon/sequencing-data/blob/main/shipment/batch-002/run-information-batch-002_column-descriptions.csv is "dna_quant", not "dna_quantity_after_extraction"
2. The proper name of the parameter in the https://github.com/emo-bon/sequencing-data/blob/main/shipment/batch-001/run-information-batch-001_column-descriptions.csv is "dna_quant", not "dna_quantity_after_extraction"
3. "paired" should be "PAIRED" (this is the appropriate value for the submission to ENA
4. The metadata full term "analysis" was repeated twice. Actually, what is term 20 is the "library_source" field that ENA requires for submission of reads.
5. "seq_meth" is actually the "instrument_model" in the ENA reads submission
6. Extra terms should be added: extraction_blank,pcr_blank_1,pcr_blank_2
   Those terms should be defined as:
   31,extraction_blank,correspoding extraction blank sequencing reads filename,Filename given by the sequencing centre to the sequencing reads produced by the extraction blank included in the same sequencing run as the sample,text,CDX_ABMLOSTA_1_1_HGVH5DRX3.UDI363,Sequencing,Genoscope; Ioulia Santi,Optional (O),,
   32,pcr_blank_1,correspoding 1st pcr blank sequencing reads filename,Filename given by the sequencing centre to the sequencing reads produced by the 1st PCR sequencing blank included in the same sequencing run as the sample,text,CEB_DCXOSTA_1_1_HGVH5DRX3.UDI363,Sequencing,Genoscope; Ioulia Santi,Optional (O),,
   33,pcr_blank_2,correspoding 2nd pcr blank sequencing reads filename,Filename given by the sequencing centre to the sequencing reads produced by the 2nd PCR sequencing blank included in the same sequencing run as the sample,text,CEB_DCYOSTA_1_1_HGVH5DRX3.UDI364,Sequencing,Genoscope; Ioulia Santi,Optional (O),,

@melinalou

[cpavloud]

@bulricht

[kmexter]

1-5 I can do - will inform bram when done
6 I don't understand - what you wrote is to go into the two descriptions files, but these columns do not exist in the main files so why add these? Are these columns that will be added to future batches/to these batches soon?

[cpavloud]

They should be added in the future.
The PCR blanks are especially relevant for the metabarcoding samples.

[kmexter]

OK, so then we will add those columns when we have info to put in them. We will keep this issue alive until then