update checkDuplicates

EBIvariation · Sep 5, 2022 · a5ec644 · a5ec644
1 parent 03e93db
commit a5ec644
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/eva_cttv_pipeline/evidence_string_generation/pipeline.nf b/eva_cttv_pipeline/evidence_string_generation/pipeline.nf
@@ -233,10 +233,10 @@ process checkDuplicates {
 
     script:
     """
-    (jq --arg sep \$'\t' -jr \
-        '.datatypeId,\$sep,.studyId,\$sep,.targetFromSourceId,\$sep,.variantId,\$sep,.variantFunctionalConsequenceId,\$sep,.diseaseFromSourceMappedId,\sep,.diseaseFromSource,"\n"' \
-        ${evidenceStrings} | sort | uniq -d > duplicates.tsv) \
-    || [[ -z duplicates.tsv ]]
+    jq --arg sep \$'\t' -jr \
+        '.datatypeId,\$sep,.studyId,\$sep,.targetFromSourceId,\$sep,.variantId,\$sep,.variantFunctionalConsequenceId,\$sep,.diseaseFromSourceMappedId,\$sep,.diseaseFromSource,"\n"' \
+        ${evidenceStrings} | sort | uniq -d > duplicates.tsv
+    [[ ! -s duplicates.tsv ]]
     """
 }