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The dnascope-pangenome pipeline never passed a metrics path to the Dedup algo, so the Picard-style duplicate-metrics file was never generated or collected by MultiQC. Forward an optional metrics path through build_dedup_job and, on the fastq path, write it into the existing <output>_metrics/ directory for the primary (bwa) alignment when metrics collection is enabled, mirroring the short-read dnascope pipeline. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Raise SEGDUP_MIN_VERSION from 0.5.1 to 0.7.0. v0.7.0 is the first release with the `--set KEY.PATH=VALUE` config override, which the pipeline now uses to pass `--set main.min_map_qual=30` for Ultima model bundles, lowering segdup-caller's default of 45. `cmd_segdup_caller` takes a list of overrides and emits a repeatable `--set`, matching the caller's own append semantics. Update the Dockerfile to build segdup-caller v0.9.0. Two related fixes were needed for the image to build: segdup-caller >=0.6.0 checks SENTIEON_LICENSE before parsing argv, so even `--version` exits non-zero without it. The container smoke test now sets a placeholder for the version probes, and check_version() logs and returns False instead of raising CalledProcessError, so a failing probe reaches the intended clean exit rather than a traceback. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The DNAscope Hybrid third stage realigns short-read data across the
regions targeted for hybrid variant calling, but wrote the result to
`hybrid_stage3.bam` under the temp directory, so it was discarded once
the run completed. Write it to `<output>_sr_realigned.{cram,bam}`
alongside the output VCF instead, matching the naming used by the
`_deduped` and `_mm2_sorted_*` outputs. The second calling pass reads
the same path.
The `--bam_format` flag was already declared on this pipeline and
documented, but nothing read it; it now selects the format for this
output, defaulting to CRAM.
`hybrid_stage3` gained a `reference` parameter, required for
`sentieon util sort` to emit CRAM, and a `util_sort_args` parameter for
consistency with the other alignment command builders. Its default is
empty rather than the usual `--cram_write_options
version=3.0,compressor=rans`, which recent Sentieon releases no longer
need; the remaining `util_sort_args` defaults are left alone for a
separate change.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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