Installing these packages inside a conda env will enable the pipeline to run outside the modules system. The scripts will need to do a conda activate popgenomics
conda create -n popgenomics -c bioconda -c conda-forge bwa samtools gatk bcftools minimap2 fasttree iqtree snpeff==4.3.1t jellyfish mosdepth yq picard
conda activate ./popgenomics
or make an environment.yml file
Installing these packages inside a conda env will enable the pipeline to run outside the modules system. The scripts will need to do a
conda activate popgenomicsor make an environment.yml file