Updated README.md with dependencies and instructions for running examples on the command line.

README.md

 # pipelines
 
-Minimal pipeline examples for IV110/IV114 at FI MUNI
+## Minimal pipeline examples for IV110/IV114 at FI MUNI
\ No newline at end of file
+
+### Dependencies
+
+- make
+- nextflow
+- snakemake
+- clustalw
+- EMBOSS cons (as em_cons command)
+- R
+- R/Bioconductor seqLogo and Biostrings packages
+
+### Instructions to run examples
+
+make all
+
+nextflow run main.nf
+
+snakemake -p set{1,2,3}.fasta_cons.fa
+