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NMRL / Ardetype

Pipeline allows to perform reference-guided de-novo assembly of bacterial genomes, starting from Illumina PE150 fastq files.
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Persample tool report #22

Closed omegatro closed 1 year ago

omegatro commented 1 year ago

Added per-sample report generation in aggregation rule of bact_shape. The logs will be updated every time aggregation rule is run, which means every time the pipeline is run not in dry-run mode.

Closes #20

omegatro commented 1 year ago

Also solves #17 by moving cgmlst database mappings for Chewbbaca and cgmlstfinder to config file.