Publication date
September 2022
DOIAbstract
[installation]: Downgraded scipy (scipy<1.9) in order to handle (https://github.com/biocore/scikit-bio/issues/1818) for installation of scikit-bio [installation]: Fix sourmash to be sourmash<4.4 due to issues with sourmash search poducing empty CSV files in some cases. [installation]: Fixed bcftools==1.13 and htslib==1.13 so that appropriate command-line parameters (filling tags with -t TYPE) work. This restriction could later be removed. [analysis]: Fixed up order of conda channels for Snakemake pipeline dependencies (was causing installation issues). [analysis]: Fixed bug with ambiguous character (N) in indel and adjusted iqtree parameters to just use the maximum specified threads instead of measuring optimal threads
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