diff --git a/tools/mitoz_annotate/mitoz_annotate.prepare.report.R b/tools/mitoz_annotate/mitoz_annotate.prepare.report.R index 6ee81bed684b41cbf6595be5c8df485cb5faf0e8..c58619693e592d3a2f560607b9f4f2a53ab1182c 100755 --- a/tools/mitoz_annotate/mitoz_annotate.prepare.report.R +++ b/tools/mitoz_annotate/mitoz_annotate.prepare.report.R @@ -2,10 +2,11 @@ library(yaml) args = commandArgs(trailingOnly=TRUE) parameters = read_yaml(args[1])$params - -if (parameters$SeOrPe == "PE") { - annotate_dir = parameters$<step_name>__mitoz_annotate_PE_output_dir - annotate_results_dir = "mitoz_annotate_PE.result" +if (exists("parameters$SeOrPe")) {#in case of minion reads this will be absent + if (parameters$SeOrPe == "PE") { + annotate_dir = parameters$<step_name>__mitoz_annotate_PE_output_dir + annotate_results_dir = "mitoz_annotate_PE.result" + } } else { annotate_dir = parameters$<step_name>__mitoz_annotate_SE_output_dir annotate_results_dir = "mitoz_annotate_SE.result"