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Regarding #14, now SalmonTE is coupled with the latest version of snakemake, so there is no more directory error. Furthermore, SalmonTE no longer runs with the older version of snakemake, please update the version of the snakemake package.
Regarding #22, mappability for each file is now reported. (MAPPING_INFO.csv in the quantification output directory)
test function has been improved, and this will give better representations of the data.
Running of SalmonTE will not produce massive and enigmatic messages anymore.