From baee202d77bd3cfb161a3ecc6274320efce94c4f Mon Sep 17 00:00:00 2001 From: Andre Date: Fri, 18 Oct 2024 22:27:07 -0400 Subject: [PATCH] Test_2: Pipeline --- pipeline/PharmCAT_Pipeline.wdl | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/pipeline/PharmCAT_Pipeline.wdl b/pipeline/PharmCAT_Pipeline.wdl index 11e5415..c588934 100644 --- a/pipeline/PharmCAT_Pipeline.wdl +++ b/pipeline/PharmCAT_Pipeline.wdl @@ -261,8 +261,8 @@ task pipeline_task { # echo "Running: $cmd" >> files/log.txt # eval $cmd - # VCFs_list="files/VCFs_list.txt" - # touch $VCFs_list + VCFs_list="files/VCFs_list.txt" + touch $VCFs_list echo "Run PharmCAT Pipeline" >> $log_file @@ -279,6 +279,7 @@ task pipeline_task { # Option 2: None VCF or TSV input. Check directory content to process elif [[ -z "~{vcf_file}" ]]; then echo "Processing all individual VCF files in the directory" >> $log_file + ls files/VCFs_inputs/*.vcf.* >> $VCFs_list # Create list with all vcf in the directory # Run all vcf files in the diretory individually @@ -306,7 +307,7 @@ task pipeline_task { } runtime { - docker: "pgkb/pharmcat:${docker_version}" # Use the user-specified or default Docker version + docker: "pgkb/pharmcat:${docker_version}" memory: max_memory cpu: max_concurrent_processes }