Repository navigation

Release/0.7.1 - #60

Draft

qclayssen wants to merge 73 commits into

mainfrom

release/0.7.1

Draft

Release/0.7.1#60
qclayssen wants to merge 73 commits into
mainfrom
release/0.7.1

Commits on Oct 2, 2025
- Make sigrap (HRDetect, MutationalPatterns) individual process (#16)
  qclayssen
  committed
  5b0598d
- linting
  qclayssen
  committed
  bcfcca0
- run more linting markdown and pre-commit
  qclayssen
  committed
  26e3758
Commits on Oct 7, 2025
- add citation doi
  qclayssen
  committed
  b2ff432
- pcgr 2.2.1 for sash (#17)
  qclayssen
  authored
  1054bfc
- add process and config for vcf2maf (#15)
  qclayssen
  authored
  f9a96bb
Commits on Oct 8, 2025
- Merge branch 'main' into release/0.7.0
  qclayssen
  committed
  acea52a
- fix typo
  qclayssen
  committed
  dc2fc10
Commits on Oct 24, 2025
- remove debug command
  qclayssen
  committed
  595e542
- 0.70 test dependancy (#36)
  qclayssen
  authored
  9c4bbff
Commits on Oct 31, 2025
- remove trailing whitespace
  qclayssen
  committed
  921f422
- add XDG_CACHE_HOME path, solve issue sigven/pcgr#246
  qclayssen
  committed
  b017b56
Commits on Nov 6, 2025
- change path of XDG_CACHE_HOME modules to general env
  qclayssen
  committed
  5e46654
- bump sigrap version to dev 7
  qclayssen
  committed
  74c3522
- bump gpgr dev version 14
  qclayssen
  committed
  116421e
Commits on Nov 7, 2025
- Feat/prepare reference (#38)
  qclayssen
  authored
  265faaf
Commits on Nov 17, 2025
- Convert dragen dir paths to file objects (#12)
  
  alexiswl
  authored and
  qclayssen
  committed
  f9c4a64
- update path vep_dir
  qclayssen
  committed
  672c302
Commits on Nov 24, 2025
- bump and synchronised bolt version
  qclayssen
  committed
  99aa12a
Commits on Nov 25, 2025
- bump bolt version 0.3.0-dev-20
  qclayssen
  committed
  39abd73
- revert gpgr container version
  qclayssen
  committed
  d8365a2
Commits on Dec 18, 2025
- bump bolt version
  qclayssen
  committed
  5f01cf1
Commits on Dec 19, 2025
- add label to process affected by hypermutated sample
  qclayssen
  committed
  b9f152a
- bump bolt dev version to 27
  qclayssen
  committed
  43784fe
Commits on Dec 22, 2025
- bump bolt dev version to 27
  qclayssen
  committed
  d3ea980
- change label process_low to process_medium_memory for hypermutated samples
  qclayssen
  committed
  db899ea
- add process_medium_memory label to match ica config
  qclayssen
  committed
  879ce3c
Commits on Dec 23, 2025
- fix typo
  qclayssen
  committed
  095caa3
- fix typo
  qclayssen
  committed
  6b11334
Commits on Jan 20, 2026
- change input vcf2maf to get pcgr reported variants
  qclayssen
  committed
  89fb9f9
Commits on Jan 21, 2026
- typo
  
  qclayssen
  and
  Copilot
  authored
  ec18125
- typo abd chord input file check exist
  qclayssen
  committed
  a854a20
Commits on Mar 19, 2026
- fix stub for vcf2maf
  qclayssen
  committed
  98b6ec1
Commits on Mar 24, 2026
- add meta data to pcgr_pass_vcf from BOLT_SMLV_SOMATIC_REPORT
  qclayssen
  committed
  6cb5d38
Commits on Mar 25, 2026
- remove dupliate channel
  qclayssen
  committed
  23f2d5c
Commits on Mar 26, 2026
- add reference ensemble genome use by PCGR for VCF2MAF
  qclayssen
  committed
  00a881e
Commits on Mar 27, 2026
- add meta data mapping
  qclayssen
  committed
  33ff6d0
Commits on May 7, 2026
- chore: bump cancer_report container to bolt:0.3.0-dev-gpgr
  qclayssen
  committed
  1264cae
Commits on May 12, 2026
- Update bolt cancer_report container to ghcr.io/umccr/bolt:0.3.0-dev-29-gpgr
  qclayssen
  committed
  3fc9764
Commits on May 13, 2026
- Bump version: 0.6.3 → 0.7.0
  qclayssen
  committed
  5e33d42
- Bump all bolt containers to ghcr.io/umccr/bolt:0.3.0-dev-29
  qclayssen
  committed
  e0d37b6
- update change log
  qclayssen
  committed
  b246d5a
- remove chord, input now from OA
  qclayssen
  committed
  dfb703a
- remove fasta_ensembl now from tarball
  qclayssen
  committed
  949608c
- fix id to tumor id
  qclayssen
  committed
  28331e6
- bump bolt version to dev-30
  qclayssen
  committed
  57e96fa
- Add addEnsemblFasta for cleaner prepare_reference
  qclayssen
  committed
  7e088fb
- add assert size and remove misc_data channel
  qclayssen
  committed
  fed190e
Commits on May 15, 2026
- Bump all bolt containers to
  qclayssen
  committed
  b52e648
Commits on May 18, 2026
- Bump all bolt containers to ghcr.io/umccr/bolt:0.3.1
  qclayssen
  committed
  35c0254
- allow explicit DRAGEN VCF paths in samplesheet (#53)
  qclayssen
  authored
  27cb5c4
Commits on May 19, 2026
Commits on May 21, 2026
- update changelog with PCGR
  qclayssen
  committed
  e514647
Commits on May 22, 2026
- bump sigrap version
  qclayssen
  committed
  556d5f6
Commits on Jul 6, 2026
Commits on Jul 13, 2026
- Merge remote-tracking branch 'origin/main' into release/0.7.0
  qclayssen
  committed
  8015ae5
Commits on Jul 17, 2026
- chore: bump version to 0.7.1 (bolt 0.3.2)
  qclayssen
  committed
  00d9f70
Commits on Jul 21, 2026
- feat!: remove plain directory input support from prepare_reference (sash #39)
  qclayssen
  committed
  05f6f49
- docs: update ADR #1 with current PCGR variant limit implementation
  qclayssen
  committed
  c223378
Commits on Jul 22, 2026
- fix: resolve merge conflicts with main (version bumps, changelog)
  qclayssen
  committed
  bf8939a
- sash: skip VCF2MAF when PCGR not emitted for high-variant-count samples (#59)
  qclayssen
  authored
  e210eaf
Commits on Jul 31, 2026
- fix(bolt): guard PCGR html mv when PCGR skipped for high-variant-count samples
  qclayssen
  committed
  4278a5e
Commits on Aug 4, 2026
- docs: fix stale 500k hypermutation threshold, clarify flag vs TMB impact
  qclayssen
  committed
  3951d72
Commits on Aug 5, 2026
- fix(pave): eliminate SIGPIPE/pipefail race in MNV guard
  qclayssen
  committed
  e2686e8
Commits on Aug 7, 2026
- test: add real (non-stub) nf-test for BOLT_SMLV_SOMATIC_REPORT mv guard
  qclayssen
  committed
  b6cdbaa

Commits

Commits on Oct 2, 2025

Commits on Oct 7, 2025

Commits on Oct 8, 2025

Commits on Oct 24, 2025

Commits on Oct 31, 2025

Commits on Nov 6, 2025

Commits on Nov 7, 2025

Commits on Nov 17, 2025

Commits on Nov 24, 2025

Commits on Nov 25, 2025

Commits on Dec 18, 2025

Commits on Dec 19, 2025

Commits on Dec 22, 2025

Commits on Dec 23, 2025

Commits on Jan 20, 2026

Commits on Jan 21, 2026

Commits on Mar 19, 2026

Commits on Mar 24, 2026

Commits on Mar 25, 2026

Commits on Mar 26, 2026

Commits on Mar 27, 2026

Commits on May 7, 2026

Commits on May 12, 2026

Commits on May 13, 2026

Commits on May 15, 2026

Commits on May 18, 2026

Commits on May 19, 2026

Commits on May 21, 2026

Commits on May 22, 2026

Commits on Jul 6, 2026

Commits on Jul 13, 2026

Commits on Jul 17, 2026

Commits on Jul 21, 2026

Commits on Jul 22, 2026

Commits on Jul 31, 2026

Commits on Aug 4, 2026

Commits on Aug 5, 2026

Commits on Aug 7, 2026