diff --git a/tasks/gene_typing/task_resfinder.wdl b/tasks/gene_typing/task_resfinder.wdl index ae9feab85..b2c9fbfd1 100644 --- a/tasks/gene_typing/task_resfinder.wdl +++ b/tasks/gene_typing/task_resfinder.wdl @@ -114,10 +114,10 @@ task resfinder { grep -qi "sulfamethoxazole" RESFINDER_PREDICTED_PHENO_RESISTANCE.txt && \ grep -qi "ampicillin" RESFINDER_PREDICTED_PHENO_RESISTANCE.txt; then echo "XDR Shigella based on predicted resistance to ceftriaxone, azithromycin, ciprofloxacin, trimethoprim, sulfamethoxazole, and ampicillin. Please verify by reviewing ~{samplename}_pheno_table.tsv and ~{samplename}_ResFinder_results_tab.tsv" - echo "XDR" > RESFINDER_PREDICTED_XDR_SHIGELLA.txt + echo "XDR Shigella" > RESFINDER_PREDICTED_XDR_SHIGELLA.txt else - echo "Not XDR" - echo "Not XDR" > RESFINDER_PREDICTED_XDR_SHIGELLA.txt + echo "Not XDR Shigella" + echo "Not XDR Shigella" > RESFINDER_PREDICTED_XDR_SHIGELLA.txt fi # set output strings for Resistance or no Resistance predicted for each of 6 drugs