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Mutect2 WDL and GetSampleName can handle multiple sample names in BAM headers #8859

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merged 2 commits into from
Jun 4, 2024

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davidbenjamin
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@davidbenjamin davidbenjamin commented Jun 3, 2024

@rickymagner we need this for Infogain.

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Just a minor comment but looks good otherwise. How many other tools depend on this one, and would any of them possibly break with a multi-sample bam input?

scripts/mutect2_wdl/mutect2.wdl Outdated Show resolved Hide resolved
@davidbenjamin
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The change doesn't affect anything when the BAM has a single sample, and when the BAM has more than one it handles what was previously a failure. So it's not going to break anything other than a pipeline that was somehow relying on the failure.

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That's a good point. Looks good to me, thanks!

@davidbenjamin davidbenjamin merged commit 2878ce5 into master Jun 4, 2024
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@davidbenjamin davidbenjamin deleted the db_sample_names_in_m2_wdl branch June 4, 2024 13:45
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2 participants