Feat/sample file format + metadata propagation

Ferlab-Ste-Justine / Post-processing-Pipeline

Variant analysis for genome and exome VGCFs

Apache License 2.0

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Closed FelixAntoineLeSieur closed 3 months ago

FelixAntoineLeSieur commented 3 months ago

Changed the expected input format of the samplesheet as discussed on notion.

We now expect a CSV file, with exactly 5 columns per sample (header required):

familyID	sampleID	sequencingType	file

A metadata block (familyID, sampleID, sequencingType, number of samples) now follow the channel for each function across the pipeline.

The pipeline still works with the same functions as before, we still need to separate them in modules.

FelixAntoineLeSieur commented 3 months ago

Tested on juno