bcf-wdl
WDL workflows for running patched bcftools against VCFs streamed directly from GCS, without silent data corruption.
The problem
htslib’s libcurl backend has no retry logic for transient HTTP errors. When streaming a VCF from GCS and the connection blips, htslib silently returns a truncated read instead of propagating the error. Worse, bcftools’ synced reader swallows I/O errors from htslib and exits 0, producing silently truncated output with no indication that anything went
This is a companion discussion topic for the original entry at github.com/broadinstitute/bcftools-patched/bcftools-merge