outdated manual at https://hq-1.gitbook.io/mc

[mbatiuk]

manual is outdated at https://hq-1.gitbook.io/mc

Such as there is no mentioning about alternative to bismark hisat3n in the reference section: https://hq-1.gitbook.io/mc/prepare/prepare-mapping-config/prepare-reference-files

However hisat3n is an option in the parameters for yap default-mapping-config

--hisat3n_dna_ref HISAT3N_DNA_REF
Path to the hisat-3n DNA reference (default: None)
--hisat3n_rna_ref HISAT3N_RNA_REF
Path to the hisat-3n RNA reference (default: None)

Github env.yaml also mentions more up to date packages for environment setup than guidline on https://hq-1.gitbook.io/mc/installation, as well as alternative environment hisat3n_env.yml