Collect query_ids into a file for FILTER_QUERY

modules/local/filter_query/main.nf

@@ -22,27 +22,19 @@ process FILTER_QUERY {
     def out_delimiter = out_format == "tsv" ? "\t" : (out_format == "csv" ? "," : out_format)
     def out_extension = out_format == "tsv" ? 'tsv' : 'csv'
 
-    // Write the query IDs to a temporary file
-    def queryFile = file("query_ids.txt")
-    queryFile.text = query_ids.join("\n")
-
     """
     # Filter the query samples only; keep only the 'id' and 'address' columns
     csvtk grep \\
         ${addresses} \\
         -f 1 \\
-        -P ${queryFile} \\
+        -P ${query_ids} \\
         --delimiter "${delimiter}" \\
         --out-delimiter "${out_delimiter}" | \\
     csvtk cut -f id,address > ${outputFile}.${out_extension}
 
-    # Remove the query_ids file after the command runs
-    rm -f ${queryFile}
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))
     END_VERSIONS
     """
 }
-

workflows/gas_nomenclature.nf

@@ -144,7 +144,7 @@ workflow GAS_NOMENCLATURE {
     ch_versions = ch_versions.mix(called_data.versions)
 
     // Filter the new queried samples and addresses into a CSV/JSON file for the IRIDANext plug in
-    query_ids = profiles.query.collect { it[0].id }
+    query_ids = profiles.query.collectFile { it[0].id + '\n' }
 
     new_addresses = FILTER_QUERY(query_ids, called_data.distances, "tsv", "csv")
     ch_versions = ch_versions.mix(new_addresses.versions)