From 49e9881c1868c1e95a0dcbf28a9daa25affc1150 Mon Sep 17 00:00:00 2001 From: Andre Date: Fri, 18 Oct 2024 23:00:56 -0400 Subject: [PATCH] Test_4: 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 bd7953a..b3f958c 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/VCFs_inputs/*.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