OA-only mode: run sash from oncoanalyser outputs only (no DRAGEN required) - #58

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qclayssen wants to merge 77 commits into

mainfrom

Commits on Oct 2, 2025

Make sigrap (HRDetect, MutationalPatterns) individual process (#16)
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5b0598d
linting
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bcfcca0
run more linting markdown and pre-commit
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26e3758

Commits on Oct 7, 2025

add citation doi
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b2ff432
pcgr 2.2.1 for sash (#17)
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1054bfc
add process and config for vcf2maf (#15)
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f9a96bb

Commits on Oct 8, 2025

Merge branch 'main' into release/0.7.0
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acea52a
fix typo
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dc2fc10

Commits on Oct 24, 2025

remove debug command
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595e542
0.70 test dependancy (#36)
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9c4bbff

Commits on Oct 31, 2025

remove trailing whitespace
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921f422
add XDG_CACHE_HOME path, solve issue sigven/pcgr#246
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b017b56

Commits on Nov 6, 2025

change path of XDG_CACHE_HOME modules to general env
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5e46654
bump sigrap version to dev 7
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74c3522
bump gpgr dev version 14
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116421e

Commits on Nov 7, 2025

Feat/prepare reference (#38)
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265faaf

Commits on Nov 17, 2025

Convert dragen dir paths to file objects (#12)

alexiswl
authored and
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f9c4a64
update path vep_dir
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672c302

Commits on Nov 24, 2025

bump and synchronised bolt version
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99aa12a

Commits on Nov 25, 2025

bump bolt version 0.3.0-dev-20
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39abd73
revert gpgr container version
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d8365a2

Commits on Dec 18, 2025

bump bolt version
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5f01cf1

Commits on Dec 19, 2025

add label to process affected by hypermutated sample
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b9f152a
bump bolt dev version to 27
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43784fe

Commits on Dec 22, 2025

bump bolt dev version to 27
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d3ea980
change label process_low to process_medium_memory for hypermutated samples
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db899ea
add process_medium_memory label to match ica config
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879ce3c

Commits on Dec 23, 2025

fix typo
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095caa3
fix typo
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6b11334

Commits on Jan 20, 2026

change input vcf2maf to get pcgr reported variants
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89fb9f9

Commits on Jan 21, 2026

typo

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and
Copilot
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ec18125
typo abd chord input file check exist
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a854a20

Commits on Mar 19, 2026

fix stub for vcf2maf
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98b6ec1

Commits on Mar 24, 2026

add meta data to pcgr_pass_vcf from BOLT_SMLV_SOMATIC_REPORT
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6cb5d38

Commits on Mar 25, 2026

remove dupliate channel
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23f2d5c

Commits on Mar 26, 2026

add reference ensemble genome use by PCGR for VCF2MAF
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00a881e

Commits on Mar 27, 2026

add meta data mapping
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33ff6d0

Commits on May 7, 2026

chore: bump cancer_report container to bolt:0.3.0-dev-gpgr
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1264cae

Commits on May 12, 2026

Update bolt cancer_report container to ghcr.io/umccr/bolt:0.3.0-dev-29-gpgr
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3fc9764

Commits on May 13, 2026

Bump version: 0.6.3 → 0.7.0
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5e33d42
Bump all bolt containers to ghcr.io/umccr/bolt:0.3.0-dev-29
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e0d37b6
update change log
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b246d5a
remove chord, input now from OA
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dfb703a
remove fasta_ensembl now from tarball
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949608c
fix id to tumor id
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28331e6
bump bolt version to dev-30
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57e96fa
Add addEnsemblFasta for cleaner prepare_reference
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7e088fb
add assert size and remove misc_data channel
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fed190e

Commits on May 15, 2026

Bump all bolt containers to
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b52e648

Commits on May 18, 2026

Bump all bolt containers to ghcr.io/umccr/bolt:0.3.1
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35c0254
allow explicit DRAGEN VCF paths in samplesheet (#53)
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27cb5c4

Commits on May 19, 2026

Commits on May 21, 2026

update changelog with PCGR
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e514647

Commits on May 22, 2026

bump sigrap version
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556d5f6

Commits on Jul 6, 2026

Commits on Jul 16, 2026

feat: add OA-only mode (no dragen required)
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bb7b75f
fix: pass oa_only channel directly into groupByMeta
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b02df68
refactor: remove all dragen inputs from oa-only branch
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711661c
fix: update example samplesheet to OA-only format
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8701612
test: rewrite prepare_input tests for OA-only mode
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61fef69
fix name pave using tumor_id
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515e277
fix: handle missing CPSR HTML in germline report when zero variants pass
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ba7b839
chore: drop orphan smlv_somatic rescue module
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0cefd2b
refactor: remove remaining dragen traces from OA-only modules
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0e5f54b
fix: drop dragen placeholder from BOLT_SMLV_SOMATIC_REPORT channel
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d9f99dd
fix: require normal_id and correct PAVE germline VCF path in OA-only mode
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021e5b5
fix: revert PAVE germline VCF path to tumor_id, not normal_id
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45b64ea

Commits on Jul 22, 2026

fix: merge main into oa-only (resolve conflicts, keep OA-only changes)
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b6b78cb

Commits on Aug 4, 2026

Merge origin/main into oa-only
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c5e04bd