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upgrade 0.7.0 #13

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qclayssen
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@qclayssen qclayssen commented Aug 18, 2025 •
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Individual PR

ready

  • PCGR 2.1
  • Split process sigrap
  • Hypermutation handling
  • Add VCF2MAF slack
  • OA V2.2.0 support

Change outside of Sash

  • Add reference data to prod
  • Update ICAv2
  • Update gpgr
  • Update sigrap

@qclayssen
add sigrap modules
ed9c127
@qclayssen
changes images modules
8914f8e
@qclayssen
uptade workflow with modules a channels
03c2cf3
@qclayssen
fix typo
e8bf9d3
@qclayssen
fix input module
ab0d3b9
@qclayssen
replace gridss by esvee data
0011e47
@qclayssen
change input channel files in subworkflow
9da48e7
@qclayssen
fix meta channel
033af83
@qclayssen
fix add tbi esvee files
c9136cf
@qclayssen
add esvee module
3e5399a
@qclayssen
update purple
4e34cbe
@qclayssen
fix image purple
7f2abbd
@qclayssen
upgrade docker image and add env
6a2a031
@qclayssen
fix linx somatic
ab5a210
@qclayssen
fix purple input doesn't take sv_tumor_unfiltered_vcf
cd22e5e
@qclayssen
change dicker image bolt
a0a2bbd
@qclayssen
fix docker path
736c478
@qclayssen
chane docker path linx report
48a153c
@qclayssen
change add eSVee call
af2e69c
@qclayssen
fix name channel
4492f56
@qclayssen
fix typo
c084de2
@qclayssen
fix fonction call
d27f6ee
@qclayssen
remove index esvee channel
1d23905
@qclayssen
add dockerfile eSVee
ae3becd
@qclayssen
change container esvee
015d5ab
@qclayssen
remove gripss filtering subworkflow and modules
6bf2d12
@qclayssen
change docker image cancer report
3996a97
@qclayssen
fix output path esvee
81ebfe5
@qclayssen
fix output path esvee
3b9e0ab
@qclayssen
fix output path eSVee
db8a53f
qclayssen and others added 22 commits July 2, 2025 16:58
@qclayssen
smlv somatic subworkflow
fb7603d
@qclayssen
add chord container
5c97eb1
@qclayssen
update pcgr report name name
dc31e4f
@qclayssen
add back missing channel
667ebf5
@qclayssen
add back sigrap process
e6b58aa
@qclayssen
change bolt version
0ec617f
@qclayssen
fix channels names
fba542c
@qclayssen
fix channel
e570e55
@qclayssen
test fix sigrap process
9a31fc0
@qclayssen
remove subworkflow
1f2c1bb
@qclayssen
update input workflow to include chord prediction from OA
a50fe9f
@qclayssen
refactor: restore publishDir for SIGRAP processes and update chord fi…
875a014 
…le reference
@qclayssen
fix and test chord
e03ca32
@qclayssen
test fix channel
268eb51
@qclayssen
remove debug commands
e2a1f15
@qclayssen
fix output MUTPAT
788587d
@qclayssen
change path VEP ref data
f56a810
@qclayssen
Chord result from OA
335fab8
@qclayssen
update container version
cee1216
@alexiswl
Convert dragen dir paths to file objects (#12)
c7fff3b
@qclayssen
Merge branch 'main' of github.com:umccr/sash
b695033
@qclayssen
Merge branch 'main' into 0.7.0
fb59922
@qclayssen qclayssen self-assigned this Aug 26, 2025
@qclayssen qclayssen mentioned this pull request Aug 26, 2025
Merged
@qclayssen qclayssen mentioned this pull request Sep 15, 2025
Merged
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@qclayssen @alexiswl