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PCGR v.2.0rc - 2024 #223

Merged
merged 275 commits into from
Jun 26, 2024
Merged

PCGR v.2.0rc - 2024 #223

merged 275 commits into from
Jun 26, 2024

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sigven
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@sigven sigven commented Apr 29, 2024

  • Functionality to support new reference data management
  • Functionality to support RNA-seq (bulk) expression input - correlation against reference samples (TCGA/DepMap/Treehouse), preliminary outlier detection (TCGA only)
  • Functionality to support VEP cache as a separate entity from the PCGR reference data
  • New copy number input format - absolute, allele-specific (nMajor + nMinor)
  • Copy number annotation moved from pcgrr to Python workflow
  • Variant oncogenicity assessment (SNVs/InDels, based on VICC/ClinGen guidelines) implemented in Python workflow
  • More robust biomarker matching implemented in Python workflow - considering genomic coordinates, HGVSp entries (considering principal and non-principal matches)
  • New HTML templates - quarto-based
  • New Excel workbook output

pdiakumis and others added 30 commits November 30, 2023 21:41
@pdiakumis
dependency cleanup
e339cce
@pdiakumis
actions cleanup
df3ec57
@pdiakumis
Bump version: 1.4.6 → 1.4.1
fa8c2aa
@pdiakumis
add quarto dependency - see quarto-dev/quarto-cli#61
f1723f0
@sigven
new pipe operator and input handling
83a995c
@sigven
improved pre-reporting pipeline
39612ed
@sigven
grch37/38 example VCFS
7ac4daa
@pdiakumis
pcgrr: add rrapply dependency
4e0323b
@pdiakumis
pcgr: add yaml + pybedtools dependencies
03f961e
@pdiakumis
pcgrr: remove cpsr circular dependency
bc275a9
@pdiakumis
Merge pull request #220 from umccr/conda_update_pd1
2ff3aaf 
Conda update
@pdiakumis
pkgdown: remove cpsr dependency
ecc95ef
@pdiakumis
bumpversion: use dev part
2082477
@pdiakumis
conda: add numpy/pybedtools/cyvcf2/pyyaml to recipe itself
815c879
@pdiakumis
Bump version: 1.4.1 → 1.4.1.9000
00df8d9
@actions-user
[bot] Updating conda-lock files (v1.4.1.9000)
9c6eef2
@pdiakumis
Bump version: 1.4.1 → 1.4.1.9000
f87df40
@actions-user
[bot] Updating conda-lock files (v1.4.1.9000)
4341239
@pdiakumis
use perl-compress-raw-zlib from conda-forge
c18a661
@sigven
fixed lock files
65bf4c7
@sigven
validate RNA input
cccaf42
@sigven
adaptions to VEP 110
f20a0e7
@pdiakumis
use perl-bio-bigfile
52d0f73
@sigven
VEP lof working
b98f6c6
@sigven
Merge branch 'bundle_update_2023' of github.com:sigven/pcgr into bund…
f8c8920 
…le_update_2023
@sigven
update gnomAD tags for 110
f2f8e12
@sigven
updated VEP pick csq criteria
c809907
@sigven
cna - fix pandas dtype warning
361276b
@sigven
fix panel match and gnomad col
b60ea96
@sigven
fix CSQ patterns and biomarker retrieval
a3796c6
pdiakumis and others added 28 commits June 20, 2024 00:00
@pdiakumis
use quay.io/bioconda/base-glibc-debian-bash:3.1 for locale
0b1c336
@pdiakumis
Bump version: 1.4.1.9017 → 1.4.1.9018
4a59f52
@actions-user
[bot] Updating conda-lock files (v1.4.1.9018)
6779cc3
@pdiakumis
GHA: re-enable free-disk-space
7fc1892
@pdiakumis
Bump version: 1.4.1.9018 → 1.4.1.9019
7b3bb65
@actions-user
[bot] Updating conda-lock files (v1.4.1.9019)
d495d0b
@pdiakumis
remove locale exporters
1486740
@sigven
Merge pull request #242 from sigven/locale
b141441 
Set locale to avoid apptainer warnings on HPC
@sigven
list all evidence items as tier2 when primary site is Any
514f4ca
@sigven
improved option checks/verification
fcc045e
@sigven
Assess oncogenicity criteria (OM1) through indirect evidence, adjust …
8a92b04 
…thresholds
@sigven
docs update
b190b3f
@sigven
fix civic test bug - show noncoding (e.g. TERT) biomarkers
0c9eafd
@sigven
Provide indirect evidence of oncogenicity for non-coding variants
34fb1e5
@sigven
Fixed TMB bug for zero variants case
fd88b9d
@sigven
20240621 bundle
6913fb9
@sigven
Bump version: 1.4.1.9019 → 1.4.1.9020
bb987be
@actions-user
[bot] Updating conda-lock files (v1.4.1.9020)
99981c0
@sigven
missing tcga for exp similarity output
6c198e1
@sigven
fix missing tcga in similarity exp tables
919a416
@sigven
check tcga data
440598e
@sigven
Bump version: 1.4.1.9020 → 1.4.1.9021
5fa4817
@actions-user
[bot] Updating conda-lock files (v1.4.1.9021)
8410233
@sigven
polish docs before release
651780e
@pdiakumis
update/sync README + pkgdown site
d91a383
@pdiakumis
add diff to changelog
edd0512
@pdiakumis
update links
dd88823
@sigven
Merge pull request #243 from sigven/pd_fixes
49398ab 
Documentation update
@sigven sigven merged commit 06f6d04 into master Jun 26, 2024
4 checks passed
@pdiakumis pdiakumis deleted the bundle_update_2023 branch June 27, 2024 00:01
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3 participants
@sigven @pdiakumis @actions-user