Use bioconda docker images for widely used tools. Images to be replaced in the Snakefile: - [x] bedtools:2.27 - [x] bedgraphtobigwig:4 - [x] cutadapt:1.16 - [x] kallisto:0.46.1 - [x] alfa:1.1.1 - [x] fastqc:0.11.9 - [x] samtools:1.10 - [x] bash:5.0.16 - [x] star:2.7.3a - [x] salmon:1.1.0 - [x] gffread:0.11.7