From 1615d8c0bc5717ad311d6afe309b9206c85ea406 Mon Sep 17 00:00:00 2001
From: Andre <ricoandre@hotmail.com>
Date: Sun, 20 Oct 2024 21:29:53 -0400
Subject: [PATCH] Test_10: Pipeline

---
 pipeline/PharmCAT_Pipeline.wdl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pipeline/PharmCAT_Pipeline.wdl b/pipeline/PharmCAT_Pipeline.wdl
index 9eaebba..5d50882 100644
--- a/pipeline/PharmCAT_Pipeline.wdl
+++ b/pipeline/PharmCAT_Pipeline.wdl
@@ -292,12 +292,12 @@ task pipeline_task {
     #   done < $list
 
     elif [[ -z "~{vcf_file}" ]]; then
-      if [[ $(ls files/input_directory/*.vcf.* 2>/dev/null | wc -l) -gt 0 ]]; then
-        echo "Processing all individual VCF files in the directory: files/input_directory/" >> $log_file
+      if [[ $(ls wf/data/*.vcf.* 2>/dev/null | wc -l) -gt 0 ]]; then
+        echo "Processing all individual VCF files in the directory: wf/data/" >> $log_file
 
         # Criar uma lista com todos os arquivos VCF no diretório
-        VCFs_list="files/VCFs_list.txt"
-        ls files/input_directory/*.vcf.* > $VCFs_list
+        VCFs_list="wf/VCFs_list.txt"
+        ls wf/data/*.vcf.* > $VCFs_list
 
         # Processar cada arquivo VCF individualmente
         while read -r vcf_file; do