updated documentation, readded the --no_run_chrysalis in usage, already still there in parameter handling
updated documentation, readded the --no_run_chrysalis in usage, already still there in parameter handling

trinityrnaseq/trinityrnaseq,g1o/trinityrnaseq,ssn1306/trinityrnaseq,macmanes-lab/trinityrnaseq,macmanes-lab/trinityrnaseq,trinityrnaseq/trinityrnaseq,g1o/trinityrnaseq,HPCHub/trinityrnaseq,macmanes-lab/trinityrnaseq,mr-c/trinityrnaseq,trinityrnaseq/trinityrnaseq,HPCHub/trinityrnaseq,g1o/trinityrnaseq,mr-c/trinityrnaseq,macmanes-lab/trinityrnaseq,trinityrnaseq/trinityrnaseq,macmanes-lab/trinityrnaseq,trinityrnaseq/trinityrnaseq,ssn1306/trinityrnaseq,mr-c/trinityrnaseq,g1o/trinityrnaseq,mr-c/trinityrnaseq,macmanes-lab/trinityrnaseq,mr-c/trinityrnaseq,HPCHub/trinityrnaseq,ssn1306/trinityrnaseq,g1o/trinityrnaseq,HPCHub/trinityrnaseq,ssn1306/trinityrnaseq,HPCHub/trinityrnaseq,g1o/trinityrnaseq,trinityrnaseq/trinityrnaseq,ssn1306/trinityrnaseq,ssn1306/trinityrnaseq,mr-c/trinityrnaseq,macmanes-lab/trinityrnaseq,HPCHub/trinityrnaseq,ssn1306/trinityrnaseq,mr-c/trinityrnaseq,HPCHub/trinityrnaseq,trinityrnaseq/trinityrnaseq,HPCHub/trinityrnaseq,g1o/trinityrnaseq,macmanes-lab/trinityrnaseq,g1o/trinityrnaseq,mr-c/trinityrnaseq,ssn1306/trinityrnaseq