- [x] base image - [x] reads_download - [x] fastqc - [x] trimmomatic - [x] megahit - [x] metaspades - [x] skesa - [x] spades - [x] pilon - [x] card_rgi - [x] mash_patlas - [x] bowtie2_samtools - [x] mapping_patlas - [x] kraken - [x] remove_host - [x] midas_species - [ ] chewbbaca - [x] mlst - [x] patho_typing - [x] seq_typing