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Merge dev changes #27

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Merged
DonFreed merged 5 commits into from
Jul 21, 2026
Merged

Merge dev changes #27

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f75a933
Emit Dedup metrics for MultiQC collection
DonFreed Jul 7, 2026
6205615
Require segdup-caller v0.7.0 and tune min_map_qual for Ultima
DonFreed Jul 20, 2026
abf72df
Expose the hybrid third-stage alignment as a pipeline output
DonFreed Jul 21, 2026
db1541c
Remove the old `docs` folder
DonFreed Jul 21, 2026
46a917a
Bump version
DonFreed Jul 21, 2026
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10 changes: 5 additions & 5 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -26,9 +26,9 @@ ARG EXPANSIONHUNTER_SHA256=ebf3ec0ace6e6e3bbce12c26463da5d9f8e16374eff1ad10f0f1a
ARG T1K_VERSION=1.0.9
ARG T1K_GIT_TAG=v1.0.9
ARG T1K_COMMIT=9376b555c1d8d2f8ca357c2656f49f450462dbc3
ARG SEGDUP_CALLER_VERSION=0.5.1
ARG SEGDUP_CALLER_GIT_TAG=v0.5.1
ARG SEGDUP_CALLER_COMMIT=0406ea78b7ff53d7a169b9aa945d7fcc7257ff12
ARG SEGDUP_CALLER_VERSION=0.9.0
ARG SEGDUP_CALLER_GIT_TAG=v0.9.0
ARG SEGDUP_CALLER_COMMIT=37c299fe16970215712b7a4ebdf1932f923e903a
# Pinned Poetry toolchain; should match the version used to generate poetry.lock.
ARG POETRY_VERSION=2.3.4
ARG POETRY_PLUGIN_EXPORT_VERSION=1.9.0
Expand Down Expand Up @@ -291,8 +291,8 @@ RUN sentieon driver --help && \
kmc --help && \
ExpansionHunter --help && \
perl -c "$(command -v run-t1k)" && \
segdup-caller --version && \
python -c "import sys; from packaging.version import Version; \
SENTIEON_LICENSE=placeholder segdup-caller --version && \
SENTIEON_LICENSE=placeholder python -c "import sys; from packaging.version import Version; \
from sentieon_cli.sentieon_pangenome import SEGDUP_MIN_VERSION; \
from sentieon_cli.util import check_version; \
sys.exit(0 if all(check_version(c, v) for c, v in SEGDUP_MIN_VERSION.items()) else 1)" && \
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135 changes: 0 additions & 135 deletions docs/dnascope-hybrid.md
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153 changes: 0 additions & 153 deletions docs/dnascope-longread.md
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