complete sql command

ktmeaton · Apr 8, 2020 · 73008d1 · 73008d1
1 parent 623152c
commit 73008d1
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/nextflow.config b/nextflow.config
@@ -96,7 +96,7 @@ params{
 
   // SQLite q
   // sqlite_select_command = "\'SELECT AssemblyFTPGenbank FROM Master WHERE BioSampleComment NOT LIKE \"%REMOVE%\"\'"
-  sqlite_select_command = "\"SELECT BioSampleHost FROM Master WHERE (BioSampleComment NOT LIKE \'%REMOVE%\') AND (TRIM(BioSampleHost) > \'\') AND (TRIM(LOWER(BioSampleHost)) IS NOT \'missing\') AND (TRIM(BioSampleCollectionDate) > \'\') AND (TRIM(LOWER(BioSampleCollectionDate)) IS NOT \'missing\' AND TRIM(LOWER(BioSampleCollectionDate)) IS NOT \'not applicable\') \""
+  sqlite_select_command = "\"SELECT AssemblyFTPGenbank FROM Master WHERE (BioSampleComment NOT LIKE \'%REMOVE%\') AND (TRIM(BioSampleHost) > \'\') AND (TRIM(LOWER(BioSampleHost)) IS NOT \'missing\') AND (TRIM(BioSampleCollectionDate) > \'\') AND (TRIM(LOWER(BioSampleCollectionDate)) IS NOT \'missing\' AND TRIM(LOWER(BioSampleCollectionDate)) IS NOT \'not applicable\' AND TRIM(LOWER(BioSampleCollectionDate)) IS NOT \'unknown\' AND TRIM(LOWER(BioSampleCollectionDate)) IS NOT \'n/a\' ) AND (TRIM(BioSampleGeographicLocation) > '') AND (TRIM(LOWER(BioSampleCollectionDate)) IS NOT \'missing\') AND (TRIM(LOWER(BioSampleCollectionDate)) IS NOT \'missing\') AND (TRIM(AssemblyFTPGenbank) > \'\') \""
 
   // MultiQC
   multiqc_config = "$baseDir/multiqc_config.yaml"