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| bcbioBaseTestsURL | bcbioBase test data URL |
| commands | Commands log parsing functions |
| copyToDropbox | Copy files to Dropbox |
| getBarcodeCutoffFromCommands | Commands log parsing functions |
| getGTFFileFromYAML | Get GTF file path from YAML |
| getLevelFromCommands | Commands log parsing functions |
| getMetricsFromYAML | Get quality control metrics from YAML |
| getSampleDataFromYAML | Get sample data from YAML |
| getUMITypeFromCommands | Commands log parsing functions |
| importDataVersions | Import data versions |
| importProgramVersions | Import program versions |
| projectDir | Project directory |
| projectDirPattern | Project directory grep pattern |
| runDate | Run date |
| sampleDirs | Sample directories |