From 5ef1c51e310a1d37527026decdaa31b310eb709b Mon Sep 17 00:00:00 2001 From: Rebecca Asch Date: Tue, 30 Jan 2024 16:52:35 -0500 Subject: [PATCH] attempt #2 to fix ClinvarSignificance output --- .../variant_annotations_table/GvsValidateVAT.wdl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl b/scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl index a78eaac5291..86d0f9456e1 100644 --- a/scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl +++ b/scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl @@ -1019,10 +1019,10 @@ task ClinvarSignificance { risk factor uncertain significance' > expected_clinvar_classes.csv - comm -23 <(sort bq_clinvar_classes.csv) expected_clinvar_classes.csv > missing_clinvar_classes.csv + comm -23 <(sort bq_clinvar_classes.csv) expected_clinvar_classes.csv > missing_clinvar_classes.txt NUMRESULTS=$( wc -l bq_clinvar_classes.csv | awk '{print $1;}' ) # we expect this to be 13+ - NUMMISS=$( wc -l missing_clinvar_classes.csv | awk '{print $1;}' ) # we expect this to be 0 + NUMMISS=$( wc -l missing_clinvar_classes.txt | awk '{print $1;}' ) # we expect this to be 0 echo "false" > ~{pf_file} # If the result of the query has fewer than 13 rows, that means clinvar_classification must not have all the expected values @@ -1030,7 +1030,7 @@ task ClinvarSignificance { echo "The VAT table ~{fq_vat_table} has the correct values for clinvar classification" > ~{results_file} echo "true" > ~{pf_file} else - tr '\n' ', ' < missing_clinvar_classes.csv + tr '\n' ', ' < missing_clinvar_classes.txt > missing_clinvar_classes.csv echo "The VAT table ~{fq_vat_table} has missing values for clinvar classification: " > ~{results_file} cat missing_clinvar_classes.csv >> ~{results_file} fi