Fix for concat_vcf for miniwdl. Link all inputs into a single directory so that vcfs and indices are together. #77
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…ry so that vcfs and indices are together.
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Looks good to me, hopefully this takes care of the index grouping issue |
gconcepcion
approved these changes
Oct 18, 2023
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concat_vcf receives an array of vcf.gz and an array of vcf.gz.tbi. Cromwell groups each pair together in a separate inputs folder (because they were generated by the same upstream task), but miniwdl provides each input independently in its own directory, so the index isn't grouped with the VCF. This PR links all inputs together into a single directory so bcftools can find the indices.