@FileIsReadable(message = "vcf does not exist or is not readable", groups = InputValidations.class) @InputArgument(flag = "--vcf") private File vcf; @FileIsReadable(message = "output does not exist or is not readable", groups = OutputValidations.class) @OutputArgument(flag = "--out") private File output; @FileIsReadable(message = "intervalList does not exist or is not readable", groups = InputValidations.class) @InputArgument(flag = "--int") private File intervalList;
@FileIsReadable(message = "unmappedSAM does not exist or is not readable", groups = InputValidations.class) @InputArgument(order = 0, delimiter = "") private File unmappedSAM; @FileIsReadable(message = "unmappedSetBit does not exist or is not readable", groups = OutputValidations.class) @InputArgument(order = 1, delimiter = "") private File unmappedSetBit;
@FileIsReadable(message = "output does not exist or is not readable", groups = OutputValidations.class) @OutputArgument(flag = "--out") private File output; @FileIsReadable(message = "maximumLikelihood does not exist or is not readable", groups = InputValidations.class) @InputArgument(flag = "--ml") private File maximumLikelihood; @FileIsReadable(message = "expectedEC2HTSFMap does not exist or is not readable", groups = InputValidations.class) @InputArgument(flag = "--ecvcf") private File expectedEC2HTSFMap;
@FileIsReadable(message = "flatVCF does not exist or is not readable", groups = InputValidations.class) @InputArgument(flag = "--fvcf") private File flatVCF; @FileIsReadable(message = "output does not exist or is not readable", groups = OutputValidations.class) @OutputArgument(flag = "--out") private File output; @FileIsReadable(message = "affy does not exist or is not readable", groups = InputValidations.class) @InputArgument(flag = "--affy") private File ecData;
@FileIsReadable(message = "Invalid flagstatInput file", groups = InputValidations.class) @InputArgument(flag = "--input") private File input; @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @OutputArgument(flag = "--output") private File output;
@Application(name = "Cluster") @Executable(value = "$%s_MAPSPLICE_HOME/bin/cluster") public class SortByName extends Module { @NotNull(message = "clusterDirectory is required", groups = InputValidations.class) @FileIsReadable(message = "clusterDirectory does not exist or is not readable", groups = InputValidations.class) @InputArgument(delimiter = "") private File clusterDirectory; @Override public Class<?> getModuleClass() { return SortByName.class; } @Override public String getExecutable() { return String.format(getModuleClass().getAnnotation(Executable.class).value(), getWorkflowName().toUpperCase()); } public File getClusterDirectory() { return clusterDirectory; } public void setClusterDirectory(File clusterDirectory) { this.clusterDirectory = clusterDirectory; } }
@FileIsReadable(message = "Invalid input file", groups = InputValidations.class) @FileIsNotEmpty(message = "input is empty", groups = InputValidations.class) @InputArgument(delimiter = "") @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @OutputArgument(delimiter = "", persistFileData = true, mimeType = MimeType.APPLICATION_BAM_INDEX) private File output;
@FileIsReadable(message = "chromosomeIndex does not exist or is not readable", groups = OutputValidations.class) @InputArgument(order = 100, delimiter = "") private File chromosomeIndex; @FileIsReadable(message = "chromosomeHeadOutput does not exist or is not readable", groups = OutputValidations.class) @InputArgument(order = 101, delimiter = "") private File chromosomeHeadOutput; @FileIsReadable(message = "chromosomeSizesOutput does not exist or is not readable", groups = OutputValidations.class) @InputArgument(order = 102, delimiter = "") private File chromosomeSizesOutput; @FileIsReadable(message = "chromosomeNamesOutput does not exist or is not readable", groups = OutputValidations.class) @InputArgument(order = 103, delimiter = "") private File chromosomeNamesOutput;
@FileIsReadable(message = "Invalid input file", groups = InputValidations.class) @FileIsNotEmpty(message = "input is empty", groups = InputValidations.class) @InputArgument(delimiter = "") @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @OutputArgument(delimiter = "", persistFileData = true, mimeType = MimeType.APPLICATION_BAM_INDEX) private File output;
@FileIsReadable(message = "Invalid flagstatInput file", groups = InputValidations.class) @InputArgument(flag = "--input") private File input; @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @OutputArgument(flag = "--output") private File output;
@FileIsReadable(message = "junction does not exist or is not readable", groups = InputValidations.class) @InputArgument(order = 0, delimiter = "") private File junction; @FileIsReadable(message = "remainingJunctions does not exist or is not readable", groups = OutputValidations.class) @InputArgument(order = 3, delimiter = "") private File remainingJunctions; @FileIsReadable(message = "filteredJunctions does not exist or is not readable", groups = OutputValidations.class) @InputArgument(order = 4, delimiter = "") private File filteredJunctions;
@FileIsReadable(message = "junctionFile does not exist or is not readable", groups = InputValidations.class) @InputArgument(order = 0) private File junctionFile; @FileIsReadable(message = "canonicalJunctionOutput does not exist or is not readable", groups = OutputValidations.class) @InputArgument(order = 8) private File canonicalJunctionOutput; @FileIsReadable(message = "nonCanonicalJunctionOutput does not exist or is not readable", groups = OutputValidations.class) @InputArgument(order = 9) private File nonCanonicalJunctionOutput;
@FileIsReadable(message = "vcf does not exist or is not readable", groups = InputValidations.class) @InputArgument(flag = "--vcf") private File vcf; @FileIsReadable(message = "output does not exist or is not readable", groups = OutputValidations.class) @OutputArgument(flag = "--out") private File output; @FileIsReadable(message = "intervalList does not exist or is not readable", groups = InputValidations.class) @InputArgument(flag = "--int") private File intervalList;
@FileIsReadable(message = "source does not exist", groups = InputValidations.class) @InputArgument private File source; @FileIsReadable(message = "File does not exist", groups = OutputValidations.class) @NotNull(message = "Output file name is required", groups = InputValidations.class) @OutputArgument(redirect = true, persistFileData = true)
@FileIsReadable(message = "inFile is not readable", groups = InputValidations.class) @InputArgument(order = 1, delimiter = "") private File inFile; @FileIsReadable(message = "chromosomeSizes is not readable", groups = InputValidations.class) @InputArgument(order = 2, delimiter = "") private File chromosomeSizes; @FileIsReadable(message = "outFile is not readable", groups = OutputValidations.class) @OutputArgument(delimiter = "") private File outFile;
@FileIsReadable(message = "Invalid input file", groups = InputValidations.class) @InputArgument private File input; @FileIsReadable(message = "Invalid output file", groups = OutputValidations.class) @OutputArgument(redirect = true, persistFileData = true, mimeType = MimeType.TEXT_STAT_SUMMARY) private File output;
@FileIsReadable(message = "input does not exist or is not readable", groups = InputValidations.class) @InputArgument(order = 0, delimiter = "") private File input;
@FileIsReadable(message = "input file is not readable", groups = InputValidations.class) @FileIsNotEmpty(message = "input file is empty", groups = InputValidations.class) @InputArgument(description = "The BAM or SAM file to parse.") @FileIsReadable(message = "output file is not readable", groups = OutputValidations.class) @FileIsNotEmpty(message = "output file is empty", groups = OutputValidations.class) @InputArgument(description = "The BAM or SAM output file.")
@FileIsReadable(message = "clusterDirectory does not exist or is not readable", groups = InputValidations.class) @InputArgument(delimiter = "") private File clusterDirectory;
private String greeting; @FileIsReadable(message = "File does not exist", groups = OutputValidations.class) @NotNull(message = "Output file name is required", groups = InputValidations.class) @OutputArgument(redirect = true, persistFileData = true)