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TORCH-Consortium / MAGMA

A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research
https://doi.org/10.1371/journal.pcbi.1011648
GNU General Public License v3.0
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Rethink FASTQ validation and accommodate FusionFS #199

Closed abhi18av closed 5 months ago

abhi18av commented 5 months ago

This PR does the following

  1. Re-establish the dependency between SAMPLESHEET_VALIDATION and FAST_VALIDATION (and others)

  2. Improve the codebase of summarization scripts, simplication and publications of json data

  3. Tighten the retry strategy for failing FASTQs

  4. Publish the validated samplesheet to the results folder.