Update organism name normalisation function and apply more consistently - #1184
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Update the 'normalise_organism_name' to convert all non-alphanumeric characters to underscores.
Explicitly call the 'normalise_organism_name' function to get a normalised name, for consistency with other code in the package.
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Two updates:
normalise_organism_namein theutilsmodule, to also remove non-alphanumeric characters (so e.g.C. elegans->c_elegans)normalise_organism_namefunction in the QC pipeline so that normalisation is applied more consistently within theauto-processpackage.