analysis: rename to SAME_AS_INPUT_VCF, #TASK-7064, #TASK-7049

opencb · Oct 10, 2024 · 6fff2f9 · 6fff2f9
1 parent 6c30115
commit 6fff2f9
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/.../src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java b/.../src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java
@@ -1489,7 +1489,7 @@ public class RunLiftoverCommandOptions {
         @Parameter(names = {"--target-assembly"}, description = "Target assembly for lift over. Valid values: GRCh38 (for Ensembl) or hg38 (for NCBI)", required = false, arity = 1)
         public String targetAssembly;
 
-        @Parameter(names = {"--vcf-destination"}, description = "Destination path where the lifted-over VCF files will be stored. If left empty, the VCF files will be stored in the job folder. If the keyword OPENCGA_VCF_INPUT_FOLDER is used, then VCF files be stored in the same folder as the input VCF files. Otherwise, they will be stored in the specified destination path", required = false, arity = 1)
+        @Parameter(names = {"--vcf-destination"}, description = "Destination path where the lifted-over VCF files will be stored. If left empty, the VCF files will be stored in the job folder. If the keyword SAME_AS_INPUT_VCF is used, then VCF files be stored in the same folder as the input VCF files. Otherwise, they will be stored in the specified destination path", required = false, arity = 1)
         public String vcfDestination;
 
         @Parameter(names = {"--outdir"}, description = "Output dir for the job.", required = false, arity = 1)

diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java
@@ -569,7 +569,7 @@ public class FieldConstants {
     // Liftover
     public static final String LIFTOVER_GRCH38 = "GRCh38";
     public static final String LIFTOVER_HG38 = "hg38";
-    public static final String LIFTOVER_VCF_INPUT_FOLDER = "OPENCGA_VCF_INPUT_FOLDER";
+    public static final String LIFTOVER_VCF_INPUT_FOLDER = "SAME_AS_INPUT_VCF";
     public static final String LIFTOVER_FILES_DESCRIPTION = "List of VCF files to lift over";
     public static final String LIFTOVER_TARGET_ASSEMBLY_DESCRIPTION = "Target assembly for lift over. Valid values: " + LIFTOVER_GRCH38
             + " (for Ensembl) or " + LIFTOVER_HG38 + " (for NCBI)";