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Handle cortex fails in variant call script #115

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martinghunt merged 1 commit into iqbal-lab-org:master from martinghunt:cortex_no_vcf

Jul 5, 2023

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martinghunt commented Jul 5, 2023

Handle edge cases caused by bad input data:

when Cortex fails (non-zero exit code), or finishes with zero exit code but doesn't make a VCF file
input reads files or ref dir do not exist
input reads files are empty

Always tries to carry on, even if that means the final VCF file has no records, and then the inferred consensus FASTA is all Ns.

Writes error messages to stderr in capitals, so should be clear that something is wrong with the sample.

Closes #114


          Handle cortex not making VCF; also empty/nonexistent input files

f55cfc8

martinghunt merged commit 1bb159f into iqbal-lab-org:master

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