Develop #12
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Develop #12
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Previously, multi sample calling was done on the merged per sample g.vcf files. However, in rare cases, VCF files that are merged by bcftools can trigger a crash in GATK. To resolve this, the multi sample calling now uses the scattered per sample g.vcf files, so that GATK does not have to act on VCF files that were modified by bcftools. As an added advantage, using the scatters directly for the multi sample calling allows for better parallelisation.
Docker hub has started to remove unused images from free accounts, which means that it might remove images used by this pipeline without notice. Therefore the pipeline now exclusively uses images from quay.io or official repositories from docker hub, which do not have this limitation.
* Use tmp on shared filesystem for aling rule * Group up tests to reduce load on test runners * Only test small-scatter on github * Check size of created files on failure * Reduce the number of test scatters * Add new entry to changelog * Pin Snakemake version
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Checklist
.github/workflows/ci.yml file.