diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java index 2f9a1b2e4f..5cb199ece6 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java +++ b/opencga-app/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 index 0e039be003..776c898067 100644 --- 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)";