From 0572b99e9ccd75ab92d68ff13a9685d6536bf675 Mon Sep 17 00:00:00 2001
From: Andre <ricoandre@hotmail.com>
Date: Sun, 20 Oct 2024 21:56:15 -0400
Subject: [PATCH] Test_12: Pipeline

---
 pipeline/PharmCAT_Pipeline.wdl | 40 ++++++++++++++++++----------------
 1 file changed, 21 insertions(+), 19 deletions(-)

diff --git a/pipeline/PharmCAT_Pipeline.wdl b/pipeline/PharmCAT_Pipeline.wdl
index ba3c1f5..8df3458 100644
--- a/pipeline/PharmCAT_Pipeline.wdl
+++ b/pipeline/PharmCAT_Pipeline.wdl
@@ -275,25 +275,27 @@ task pipeline_task {
       echo "Running command: $cmd" >> $log_file
       eval $cmd
 
-    # # Option 2: None VCF or TSV input. Check directory content to process
-
-    # elif [[ -z "~{vcf_file}" ]]; then
-    #   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
-
-    #     VCFs_list="wf/VCFs_list.txt"
-    #     ls wf/data/*.vcf.* > $VCFs_list
-
-    #     while read -r vcf_file; do
-    #       echo "Processing individual VCF file: $vcf_file" >> $log_file
-    #       cmd="pharmcat_pipeline $vcf_file $arg"
-    #       echo "Running command: $cmd" >> $log_file
-    #       eval $cmd
-    #     done < $VCFs_list
-    #   else
-    #     echo "No VCF files found in files/input_directory. Exiting." >> $log_file
-    #     exit 1
-    #   fi
+    # Option 2: None VCF or TSV input. Check directory content to process
+
+    elif [[ -z "~{vcf_file}" ]]; then
+      # 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
+
+      #   VCFs_list="wf/VCFs_list.txt"
+      #   ls wf/data/*.vcf.* > $VCFs_list
+
+      #   while read -r vcf_file; do
+      #     echo "Processing individual VCF file: $vcf_file" >> $log_file
+      #     cmd="pharmcat_pipeline $vcf_file $arg"
+      #     echo "Running command: $cmd" >> $log_file
+      #     eval $cmd
+      #   done < $VCFs_list
+      # else
+      #   echo "No VCF files found in files/input_directory. Exiting." >> $log_file
+      #   exit 1
+      # fi
+
+      echo "dentro da opcao de diretorio" >> $log_file
 
     else
       echo "No VCF or list of VCFs provided or found in directory. Exiting." >> $log_file