Test_13: Pipeline

pipeline/PharmCAT_Pipeline.wdl

@@ -266,8 +266,11 @@ task pipeline_task {
     #   cohorts, such as UK Biobank). Input VCF files must at least comply with 
     #   Variant Call Format (VCF) Version >= 4.2.
 
+    # Resolver a variável `vcf_file` fora do bloco condicional
+    vcf_file="~{vcf_file}"
+
     # option 1: User add on VCF or TSV file in the vcf_file input
-    if [[ -n "~{vcf_file}" && -f ~{vcf_file} ]]; then
+    if [[ -n ~{vcf_file} && -f ~{vcf_file} ]]; then
       # mkdir -p data
       cp ~{vcf_file} wf/data
       echo "Processing list of VCF files as a single block from: ~{vcf_file}" >> $log_file
@@ -276,33 +279,31 @@ task pipeline_task {
       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
-
-      echo "dentro da opcao de diretorio" >> $log_file
+    elif [[ -z "$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 wf/data/. Exiting." >> $log_file
+        exit 1
+      fi
 
     else
       echo "No VCF or list of VCFs provided or found in directory. Exiting." >> $log_file
       exit 1
     fi
 
 
+
     # Run the command
     echo "Pharmcat_pipeline finished" >> $log_file