diff --git a/tasks/gene_typing/task_resfinder.wdl b/tasks/gene_typing/task_resfinder.wdl index f701d705a..d50faf870 100644 --- a/tasks/gene_typing/task_resfinder.wdl +++ b/tasks/gene_typing/task_resfinder.wdl @@ -113,8 +113,8 @@ task resfinder { grep -qi "trimethoprim" RESFINDER_PREDICTED_PHENO_RESISTANCE.txt && \ 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 ceftriazone, azithromycin, ciprofloxacin, trimethoprim, sulfamethoxazole, and ampicillin. Please verify by reviewing ~{samplename}_pheno_table.tsv and ~{samplename}_ResFinder_results_tab.tsv" - echo "XDR Shigella based on predicted resistance to ceftriazone, azithromycin, ciprofloxacin, trimethoprim, sulfamethoxazole, and ampicillin. Please verify by reviewing ~{samplename}_pheno_table.tsv and ~{samplename}_ResFinder_results_tab.tsv" > RESFINDER_PREDICTED_XDR_SHIGELLA.txt + 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 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" > RESFINDER_PREDICTED_XDR_SHIGELLA.txt else echo "Not predicted as XDR Shigella" echo "Not predicted as XDR Shigella" > RESFINDER_PREDICTED_XDR_SHIGELLA.txt