From 7dbe9ceacd2058685e711a3f103b9e2f95f6b2b0 Mon Sep 17 00:00:00 2001 From: Andre Date: Sat, 19 Oct 2024 07:49:51 -0400 Subject: [PATCH] Test_5: Pipeline --- pipeline/PharmCAT_Pipeline.wdl | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/pipeline/PharmCAT_Pipeline.wdl b/pipeline/PharmCAT_Pipeline.wdl index b3f958c..d304502 100644 --- a/pipeline/PharmCAT_Pipeline.wdl +++ b/pipeline/PharmCAT_Pipeline.wdl @@ -280,15 +280,15 @@ task pipeline_task { elif [[ -z "~{vcf_file}" ]]; then echo "Processing all individual VCF files in the directory" >> $log_file - ls files/input_directory/*.vcf.* >> $VCFs_list # Create list with all vcf in the directory - - # Run all vcf files in the diretory individually - for vcf_file in $(cat $VCFs_list); do - echo "Processing individual VCF file: $vcf_file" >> $log_file - cmd="pharmcat_pipeline $vcf_file $args" - echo "Running command: $cmd" >> $log_file - eval $cmd - done + # ls files/input_directory/*.vcf.* >> $VCFs_list # Create list with all vcf in the directory + + # # Run all vcf files in the diretory individually + # for vcf_file in $(cat $VCFs_list); do + # echo "Processing individual VCF file: $vcf_file" >> $log_file + # cmd="pharmcat_pipeline $vcf_file $args" + # echo "Running command: $cmd" >> $log_file + # eval $cmd + # done else echo "No VCF or list of VCFs provided. Exiting." >> $log_file