Release 0.3.0 + 0.3.1 (validated via ICA full-pipeline runs) - #35

Merged

qclayssen merged 63 commits into

mainfrom

release/0.3.1-validated

Jul 22, 2026

Commits on Oct 2, 2025

Add option for sash sigrap individual process input to cancer report (#11)
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d7ca46b
Hypermutation Handling in PCGR (#9)
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f33c48c
Feature/pcgr v2.2.1 (#10)
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cb5ee4d
fix merge duplication and imports
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9d8e4d1
bump pcgr version
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8db35b3
bump gpgr version
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c67b30a

Commits on Oct 16, 2025

change print to logging
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f9a7d3b
add argument chunck size
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b8ee4a0

Commits on Oct 17, 2025

fix version software pcgr container
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8223ef9
add logging and filter fonction to read value and replace placeholder
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f83c23a
fix indentation
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22b5c12
read gz tsv from pcgr
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529309c

Commits on Oct 20, 2025

change PCGR_CLINVAR_CLASSIFICATION
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d3dd182
Change pcgr header check
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a5fc923

Commits on Oct 24, 2025

tyo
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bf930e7
typo
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8ea1edc
add missing variable pcgr_output_dir
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443c5be

Commits on Nov 19, 2025

Pcgr v2.2.5 (#22)
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966967f

Commits on Nov 24, 2025

Uptade sage vcf header check (#24)
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6a93f6b
add missing HMF_HOTSPOT constant
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ed3b11b
Fix quotation
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a3d16f7
Fix test
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9ddeac8

Commits on Dec 16, 2025

remove PCGR html report from chunk (hypermutated) to reduce memory use
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41b83bb

Commits on Dec 17, 2025

Commits on Dec 19, 2025

Commits on Dec 22, 2025

Extract PCGR errors from log files
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15db538

Commits on Jan 21, 2026

Update bolt/workflows/other/cancer_report.py

qclayssen
and
Copilot
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9bf22f5
Update bolt/common/pcgr.py

qclayssen
and
Copilot
authored
599849d

Commits on Feb 19, 2026

Apply suggestions from code review

qclayssen
and
Copilot
authored
09a3a24
fix typo
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committed
dbd500f
remove duplicate fonction
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3d2d7b1

Commits on Feb 20, 2026

fix typo
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15f0247
add check pcgr_hotspot_present value
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8fa85ef

Commits on May 7, 2026

add is_hypermutated flag to variant counts process JSON
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31dabab

Commits on May 12, 2026

Commits on May 13, 2026

Commits on May 14, 2026

fix hypermutated tag
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7f01001
Add tests for is_hypermutated dragen count fix
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97ad9f7
Separate stdout/stderr streams in execute_command
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b4ab71f

Commits on May 15, 2026

Pin r-gpgr ==2.3.0 in Dockerfile.gpgr
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1b366fa
fix doc and missing file closure
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f77deb4
add test
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1b6e28a
change .with_suffix :
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58987d1
chore: untrack local-only files
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5949539
update CHANGELOG for 0.3.0 release
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e0103ef

Commits on May 18, 2026

bump version to 0.3.1 and update changelog
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149db35
ci: add smoke tests to catch image startup failures before push
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358290a

Commits on May 19, 2026

Commits on May 24, 2026

fix: bump r-gpgr to 2.3.1 in gpgr Docker image
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d2c390f

Commits on Jul 16, 2026

Merge remote-tracking branch 'origin/main' into release/0.3.1-validated
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ef00deb

Commits on Jul 21, 2026