Commit 84e27d07 authored by khalid's avatar khalid
Browse files

cases where SeorPe parameter is not set (minion)

parent 4c50a0ce
......@@ -2,10 +2,11 @@ library(yaml)
args = commandArgs(trailingOnly=TRUE)
parameters = read_yaml(args[1])$params
if (parameters$SeOrPe == "PE") {
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"
......
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