Fix non-deterministic errors in GetSampleIdsFromVcfTar #531
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cwhelan
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* Revert to CPG commit ca70123 * Absorb Broad upstream changes: * Add handling for Flag vcf fields to vcf_to_pandas (broadinstitute#506) * add outlier samples list & count outputs to PlotSVCountsPerSample (broadinstitute#510) * eliminate cram to bam conversion when possible (broadinstitute#468) * Add ref panel inputs for MakeCohortVcf subworkflows (broadinstitute#517) * Extend STR workflow to collect additional locus-level metrics (broadinstitute#516) * Change ref allele to N if unsupported in gatk formatting script (broadinstitute#511) * Add sample renaming for SD files in GatherBatchEvidence (broadinstitute#519) * Remove vcf header contig sorting in CleanVcf5 (broadinstitute#518) * Add support for building dockers for multiple registries. (broadinstitute#507) * Remove non-public images from the git-sha-based target determination (broadinstitute#525) * Fix ReadMe for build docker (broadinstitute#528) * Fix for tiny shard of IntegrateGQ in single sample pipeline (broadinstitute#524) * Fix issue in Genotype batch script with low PE_log_pval causing zero PE_count (broadinstitute#527) * Manually install MASS R package in sv-pipeline-virtual-env (broadinstitute#534) * Fix non-deterministic errors in GetSampleIdsFromVcfTar (broadinstitute#531) * Add ApplyManualVariantFilter json template (broadinstitute#536) * make the RunMELT task a little more robust (broadinstitute#529) * Improve STR workflow (broadinstitute#539) * Fix workspace format (Generate Terra workspace tsv files from transposed tables) (broadinstitute#523) * Update VaPoR workflows (broadinstitute#532) * Update README to link to SV callers used. (broadinstitute#541) Co-authored-by: Mark Walker <markw@broadinstitute.org> Co-authored-by: epiercehoffman <epierceh@broadinstitute.org>
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GetSampleIdsFromVcfTaroccasionally fails with an error about the piping strategy used. This PR simplifies the code that uses more disk but is safer and still fast.