From df524f689554174381044291eba4af96ad2f2a53 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Thu, 16 May 2024 15:18:13 -0400
Subject: [PATCH] Improvements to the FILTER_QUERY module

---
 modules/local/filter/main.nf | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/modules/local/filter/main.nf b/modules/local/filter/main.nf
index 305af37..72aacbc 100644
--- a/modules/local/filter/main.nf
+++ b/modules/local/filter/main.nf
@@ -13,7 +13,7 @@ process FILTER_QUERY {
     val out_format
 
     output:
-    path("new_addresses.csv"),  emit: csv
+    path("new_addresses.*"),    emit: csv
     path("versions.yml"),       emit: versions
 
     script:
@@ -31,12 +31,9 @@ process FILTER_QUERY {
         ${addresses} \\
         --filter '\$id == \"$queryID\"' \\
         --delimiter "${delimiter}" \\
-        --out-delimiter "${out_delimiter}" \\
-        --out-file ${outputFile}.tmp
-
-    csvtk cut -f 1,2 ${outputFile}.tmp > ${outputFile}.${out_extension}
-    rm ${outputFile}.tmp
-
+        --out-delimiter "${out_delimiter}" | \\
+    csvtk cut -f id,address > ${outputFile}.${out_extension}
+    
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))