Examples with SubStage com.hartwig.pipeline.stages.SubStage used on opensource projects

Example 1 with SubStage

use of com.hartwig.pipeline.stages.SubStage in project pipeline5 by hartwigmedical.

the class SageGermlinePostProcess method bash.

@Override
public List<BashCommand> bash(final OutputFile input, final OutputFile output) {
    final List<BashCommand> result = Lists.newArrayList();
    SubStage passFilter = new PassFilter();
    OutputFile finalOutputFile = OutputFile.of(sampleName.sampleName(), SAGE_GERMLINE_FILTERED, FileTypes.GZIPPED_VCF);
    result.addAll(passFilter.bash(input, finalOutputFile));
    return result;
}

Example 2 with SubStage

use of com.hartwig.pipeline.stages.SubStage in project pipeline5 by hartwigmedical.

the class SageSomaticPostProcess method bash.

@Override
public List<BashCommand> bash(final OutputFile input, final OutputFile output) {
    final List<BashCommand> result = Lists.newArrayList();
    SubStage passFilter = new PassFilter();
    OutputFile finalOutputFile = OutputFile.of(tumorSampleName.sampleName(), SAGE_SOMATIC_FILTERED, FileTypes.GZIPPED_VCF);
    result.addAll(passFilter.bash(input, finalOutputFile));
    return result;
}