Environments for the pipeline

cambiotraining / awd-pathogen-bioinformatics

Materials for "Introduction to Cholera Genomics" course

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Closed bsalehe closed 10 months ago

bsalehe commented 11 months ago

The following are conda environment names for the pipeline need to be created. Essentially, they are aimed for command line practicals.

[x] "assembly" - this will be used for running flye, medaka, rasusa, bakta, Mash
[x] "typing" - this will be used to run mlst, panaroo, IQ-TREE, and Figtree
[x] "nextflow" - for running AMR analysis with nf-core/funcscan
[x] "checkm" - for checking the quality of assembly

tavareshugo commented 10 months ago

These are all detailed in the data & setup