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Add a target type for indexed luigi.LocalTarget #8

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arteymix opened this issue Mar 4, 2022 · 1 comment
Open

Add a target type for indexed luigi.LocalTarget #8

arteymix opened this issue Mar 4, 2022 · 1 comment

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@arteymix
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arteymix commented Mar 4, 2022

This would apply to indexed BAMs and VCFs and possibly other tabular format with tabix. This would basically turn the folowwing:

class TaskThatProducesIndexedOutput(luigi.Task):
    def output(self):
        return luigi.LocalTarget('test.vcf.gz'), luigi.LocalTarget('test.vcf.tbi.gz')

Into:

class TaskThatProducesIndexedOutput(luigi.Task):
    def output(self):
        return bioluigi.targets.IndexedLocalTarget('test.vcf.gz')

It would be considered complete if both resulting local targets exist.

@arteymix
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arteymix commented Mar 4, 2022

This would be used in the future GATK module. It can also be readily used in the chromium-pipeline we already have to simplify some of our output/input logics.

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