revert stub_run index check skip [skip ci]#304
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Hey Rayan, thanks for spotting this. Just clarifying for option 1: adding the missing .tbi stub files means that the |
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Apologies if that wasn't clear, the 2 are unrelated: we have missing index files for the PURPLE VCFs (which was the initial issue reported) in the stub tests and the stubs don't pass right now in dev-3.0.0 (regardless) because of the missing bam index validation (for the stubs). To deal with the latter, we either reintroduce the removed logic, using something like the |
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@scwatts has taken over the OA dev work to prepare for the 3.0 release. Stephen, maybe you've encountered these issues and fixed them already in your branch? If not, could you add the missing Purple vcf tbi files in the stub definitions? And I'm in favor of adding this fix that Rayan proposed to avoid adding code that's only for stub runs:
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To deal w/ failure of stub tests that appears to be due to this commit which disabled the index validation skipped for the stub tests.
I see 2 options to deal with the matter 1) add index entries in the stub test's samplesheet for clean validation (Luân's initial idea I assume?) or 2) revert to skipping the index validation for the stub tests. If 2 is favoured, code below.
Additionally, the index files of the VCF generated by purple were not being created by the stubs (initial issue reported)
Fine w/ either option on my end!
PS: skipped all ci testing due to nf-core template mismatch & other lingering snapshots differences, etc