try file

Author: mmorgantaylor

pipelines/wdl/glimpse/low_pass_imputation/input_qc/LowPassImputationQC.wdl

@@ -164,11 +164,11 @@ task ConvertCramManifestToCramArrays {
         touch qc_messages.txt
 
         # convert the cram manifest into arrays of crams, cram indices, and sample ids
-        header=$(head -n 1 ~{cram_manifest})
+        head -n 1 ~{cram_manifest} > header.txt
 
-        sample_id_col=$(echo "${header}" | tr '\t' '\n' | grep -n "^sample_id$" | cut -d: -f1)
-        cram_path_col=$(echo "${header}" | tr '\t' '\n' | grep -n "^cram_path$" | cut -d: -f1)
-        cram_index_col=$(echo "${header}" | tr '\t' '\n' | grep -n "^cram_index_path$" | cut -d: -f1)
+        sample_id_col=$(cat header.txt | tr '\t' '\n' | grep -n "^sample_id$" | cut -d: -f1)
+        cram_path_col=$(cat header.txt | tr '\t' '\n' | grep -n "^cram_path$" | cut -d: -f1)
+        cram_index_col=$(cat header.txt | tr '\t' '\n' | grep -n "^cram_index_path$" | cut -d: -f1)
 
         if [ -z "${sample_id_col}" ] || [ -z "${cram_path_col}" ] || [ -z "${cram_index_col}" ]; then
             echo "Unable to determine column positions for sample_id, cram_path, or cram_index_path in the CRAM manifest." >> qc_messages.txt