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Fix/sigprofiler probabilities per mutation - #220

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robert-a-forsyth wants to merge 343 commits into

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fix/sigprofiler-probabilities-per-mutation

Closed

Fix/sigprofiler probabilities per mutation#220
robert-a-forsyth wants to merge 343 commits into
mainfrom
fix/sigprofiler-probabilities-per-mutation

This pull request is big! We're only showing the most recent 250 commits

Commits on Sep 14, 2026
Commits on Sep 15, 2026
Commits on Sep 16, 2026
- Re-sync the vendored lrsomatic_report to v1.4.0
  
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- Add the changelog entry for the v1.4.0 report re-sync
  
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Commits on Sep 17, 2026
- Name v1.4.0 as the vendored report version in the #176 entry
  
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- Pull the report tool from a container instead of vendoring its source
  
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- Fold the #195 changelog entry into #196
  
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  41ab645
- Run ClairS-TO's Verdict against CHM13 instead of GRCh38 only
  
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- Restore the ClairS-TO output filenames that 0.5.1 renamed
  
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  ac2812b
- Join the Verdict resource channels instead of merging them
  
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  d310ddb
- Regenerate the pipeline snapshots for ClairS-TO 0.5.1
  
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  5993fd6
- Run ClairS-TO once per tumour-only sample on CHM13
  
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- Trim inline comments in the files this PR touches
  
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  663550c
- Find the Verdict resource files inside the directory UNZIP hands over
  
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- Address review on #196: sandbox XDG_CACHE_HOME, meta.yml version key
  
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  469e3a3
- Take lrsomatic_report 1.5.1, for the stale panel_hit cell
  
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- Name the 1.5.1 report container in the changelog
  
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  317337f
- Take lrsomatic_report 1.6.0 and rebuild the lymphoid panel
  
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  1ce36a3
- Fix review findings on the lymphoid panel and the version eval
  
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Commits on Sep 18, 2026
- Pin the ClairS-TO image that CI can actually read
  
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  cc2eb06
- Reconcile the lymphoid row count in the changelog
  
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  2b93aea
- Merge pull request #196 from IntGenomicsLab/feat/containerise-lrsomatic-report
  ljwharbers
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  f3e3fbb
- make passing variants the only form pushed through to downstream analysis in Deepvariant by default (toggleable)
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  59c2216
- Tag ClairS-TO calls from ASCAT's purity and copy number when ASCAT runs
  
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  8ec352a
- Merge origin/dev into the ClairS-TO Verdict CHM13 branch
  
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  500e9c0
- Say in the docs what --skip_ascat's purity estimate is still worth
  
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  eb09016
- Build the Verdict resource set only when ClairS-TO reads it
  
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  a58d1f2
- Publish the tables Verdict tagged from on --skip_ascat runs too
  
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  8a3d5ca
- Cover both germline tagging paths with a stub nf-test
  
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  8a63f78
- fixes to the filtering
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  c596e1b
Commits on Sep 21, 2026
- Merge pull request #197 from IntGenomicsLab/feat/clairsto-verdict-chm13
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  17b22e2
- Trim the v1.2.0dev changelog entries to one to three sentences
  
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  580c3b7
- Shorten comments in helper scripts, module metadata, tests and CI
  
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  372dfeb
- Trim prose in Nextflow comments and error messages
  
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  912318c
- Dedupe and shorten the docs and parameter help text
  
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  876822c
- Restore pr-comment.yml to the template version
  
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  4ca296b
- Revert the nf-test and template-version-comment workflows to dev
  
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  d802492
- testing
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  9a1e8e6
- Merge pull request #198 from IntGenomicsLab/chore/concise-comments
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  7dabdab
- fix bugs
  robert-a-forsyth
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  938f084
- Merge origin/dev into add-savana-module
  
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  94ef848
- Fix VEP_SAVANA call for dev's new ENSEMBLVEP_VEP signature; regenerate snapshots
  
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  23fa027
- Run the CPU-only rebuild of the ClairS-TO fork image
  
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Commits on Sep 22, 2026
- Merge pull request #199 from IntGenomicsLab/fix/clairsto-cpu-image
  ljwharbers
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  8b4ebce
- bump wakhan (bug)
  robert-a-forsyth
  committed
  5b38dcf
- Merge remote-tracking branch 'origin/dev' into variant_filter
  robert-a-forsyth
  committed
  1f93364
- Split multi-allelics before intersection, harden the consensus channel joins
  
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  da99d0b
- Adjudicate the tumour-only germline arm with DeepSomatic's verdict
  
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  b646c20
- Preserve the caller's FILTER through VCFTAG so the PASS filter still bites
  
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  33bb9b2
- Make the VCFTAG test runnable
  
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  33a631b
- Fold STANDARDIZE_AF into BCFTOOLS_ANNOTATE
  
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  825af15
- Drop a duplicated CLAIR3 argument and correct a false ordering comment
  
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  d4401a4
- Merge pull request #189 from YannVRB/add-savana-module
  ljwharbers
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  313cc4a
- Pull the ClairS-TO image as docker:// under Singularity and Apptainer
  
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  601ed02
- Record the ClairS-TO docker:// switch in the changelog
  
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  9922196
- Pull the ClairS-TO image from Docker Hub instead of ghcr
  
  ljwharbers
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  d93e6bf
- Merge pull request #201 from IntGenomicsLab/fix/clairsto-docker-pull
  ljwharbers
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  0cf00bf
- Regenerate snapshots for the germline/somatic tagging processes
  
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  d3b4581
- Merge remote-tracking branch 'origin/dev' into variant_filter
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Commits on Sep 23, 2026
- fix report clog
  robert-a-forsyth
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  25a0191
- Fill in the PR number on this branch's changelog entries
  
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  0a3024a
- Merge remote-tracking branch 'origin/dev' into variant_filter
  robert-a-forsyth
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  2d4e9ce
- Satisfy the pre-commit hooks: call the report slot closure explicitly
  
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  d5e610e
- Let ClairS phase internally: its input BAM is not haplotagged
  
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  8b6483d
- Correct ClairS SNV output name in docs/output.md
  
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  89de9fd
- Fill in PR number in CHANGELOG entries
  
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Commits on Sep 24, 2026
- Add ecDNA analysis: CoRAL reconstruction and AmpliconClassifier
  
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  1376557
Commits on Sep 25, 2026
- Merge pull request #203 from IntGenomicsLab/fix/clairs-untagged-bam
  AmberVerhasselt
  authored
  4d5fcdb
- fixes ecDNA subworkflow
  robert-a-forsyth
  committed
  001926c
- Download ClinVar once in PREPARE_VEP_PLUGINS, pinned by MD5
  
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  07473cc
- Move the INFO/SOMATIC filter of local BCFTOOLS_VIEW into ext.args
  
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  27728f8
- Leave FILTER untouched in VCFTAG
  
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  c691a0c
- Prefilter DS_VERDICT_QUERY to the non-PASS/RefCall DeepSomatic rows
  
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  75036a0
- Rejoin split multi-allelics after the caller consensus
  
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  18023f2
- Join ASCAT and Wakhan report files instead of counting with groupKey
  
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  6a3e297
- Report VEPPLUGIN_CLINVAR's version through versions.yml, not eval()
  
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  941567f
- Inline the PASS filter as BCFTOOLS_VIEW aliases at each caller
  
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  d653bcb
- Add VCFTAG meta.yml and fix var_keep defaults in usage.md
  
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  c91a23e
- Allow deepvariant without deepsomatic; skip the verdict transfer then
  
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  5fae932
- Cut long comments, sample numbers and CHANGELOG write-ups to one or two lines
  
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  00a9312
- Regenerate pipeline snapshots after the review fixes
  
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  ff88896
- Fill in PR number in CHANGELOG entry
  
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  3962825
- Address review on #206: fetch only http(s)/ftp, pin the CHM13 index
  
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  a327baa
- Merge pull request #206 from AmberVerhasselt/fix/clinvar-prepare
  AmberVerhasselt
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  6c553bc
Commits on Sep 28, 2026
- Merge remote-tracking branch 'origin/dev' into coral
  
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  219aaaf
- Merge dev into variant_filter
  
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  7692333
Commits on Sep 29, 2026
- Phase only alt somatic records, without germline records at their positions
  
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  46e9346
- Keep one caller's record per position in the 'all' caller union
  
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  97801ff
- Assert record contents of the phased VCFs in the pipeline tests
  
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  cadbdee
- Warn when tumour-only DeepVariant calls run without DeepSomatic's verdict
  
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  24404b8
- Regenerate pipeline snapshots after the review fixes
  
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  1982724
- Add Claude PR review workflow and REVIEW.md
  
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  b03b9c5
- Fill in PR number in CHANGELOG entry
  
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  72eb901
- Revert ro-crate-metadata.json churn from local lint
  
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  f6e6473
- Pin Claude review to Opus 5.5 with high effort
  
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  e263e7b
- Drop CHANGELOG entry for Claude review workflow
  
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  9a39c9c
- Merge pull request #208 from IntGenomicsLab/ci/claude-review
  ljwharbers
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  f66cadc
Commits on Sep 30, 2026
- Merge remote-tracking branch 'origin/variant_filter' into coral
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  committed
  9ce6a8a
- Find the downloaded AA data repo and surface AmpliconClassifier's log
  
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  d17aa7b
- Pin the AA data repo download by MD5 and skip AC when no repo exists
  
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  55473b0
- Warn on dropped CoRAL samples, plot the classified cycles, right-size CoRAL
  
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  a4d9ee3
- Config and docs for the review fixes
  
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Commits on Oct 1, 2026
- Stop PR comments from cancelling the Claude review
  
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  658f374
- Prefer PASS records before the caller priority in the 'all' union
  
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  f13370c
- Tag the VCFTAG and BCFTOOLS_EXCLUDE_SITES module tests small so PR CI runs them
  
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  7c5df13
- Merge pull request #211 from IntGenomicsLab/ci/claude-review-concurrency-dev
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  c17991e
- Update nf-core modules and bump local module tools
  
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  7eaede8
- Restore NanoPlot arrow input and fix missed .tbi joins
  
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  733bc23
- Rename AF tags only where the source tag exists; update snapshots
  
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  2ec2bef
- Update union snapshot
  
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  9555b5c
- Fill in PR number in CHANGELOG entry
  
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  c3ba089
- Update Clair3, ClairS, DeepVariant and DeepSomatic
  
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  0e628ff
- Restore DeepVariant edits that were missing from the patch files
  
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  7cb08bb
- Update default, chm13 and clair_only snapshots for the new callers
  
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  c1d0489
- Update consensus, deep_only and union snapshots for the new callers
  
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  69ebae2
- Fill in PR number in CHANGELOG entry
  
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  d3d4614
- Skip nf-core component tests in nextflow-lint
  
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  906aad3
- Update Wakhan to 0.5.0
  
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  6467ebe
- Fill in PR number in CHANGELOG entry
  
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  4f1c7e1
- Correct the #212 CHANGELOG entry
  
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  a47eb1f
- Re-record module snapshots for patched NanoPlot and bcftools
  
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  9688f05
- Run lrsomatic_report 1.6.1
  
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  786ef8e
- Warn instead of abort on bcftools norm REF mismatches
  
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  78fb702
- Merge branch 'chore/module-updates' into chore/variant-caller-updates
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  a8d27e6
- Address review: DeepSomatic small model, ClairS container ternary
  
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  fc0e823
- Add a WAKHAN module stub test
  
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  1ae5e77
- Merge remote-tracking branch 'origin/chore/module-updates' into feat/wakhan-0.5.0
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- Pull WAKHAN from Docker Hub, with the coverage-histogram fix
  
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Commits on Oct 2, 2026
- Keep only DeepVariant PASS calls at DeepSomatic germline sites
  
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  81085f2
- Keep one record per position within each caller in the 'all' union
  
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  ed9a7f6
- Test VCFSPLIT's ORIG_FILTER handling and keep a pre-existing ORIG_FILTER
  
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  committed
  2956721
- Split multi-allelics before the DeepSomatic verdict transfer
  
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  149e9be
- Expect an all-PASS tumour-only germline arm with the PASS filter off; regenerate snapshots
  
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  e2ab46a
- Merge pull request #213 from IntGenomicsLab/chore/variant-caller-updates
  AmberVerhasselt
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  35b41b4
- Merge origin/chore/module-updates (#213) into feat/wakhan-0.5.0
  
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  9edfb76
- Merge pull request #214 from IntGenomicsLab/feat/wakhan-0.5.0
  AmberVerhasselt
  authored
  f8a8dc5
- Add optional whitelist Severus calling (--severus_whitelist)
  
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  1511db3
- Address round-2 review: CLAIR3_MODEL TLS, stub test, model checks
  
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  30d5cc6
- Address review on #215: module stub test, meta.yml outputs, CHANGELOG, help_text
  
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  393e7ce
- Merge branch 'vf-review-fixes' into coral
  robert-a-forsyth
  committed
  9fb1369
- Merge pull request #200 from IntGenomicsLab/variant_filter
  robert-a-forsyth
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  91b0e11
- Merge dev into chore/module-updates
  
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  5060eb8
- Check ASCAT purity before reading segments; treat an empty segments table as no segments
  
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  36e627f
- Pass empty SAVANA contigs/g1000 inputs without --genome; declare them as hidden params
  
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  40dd637
- Give SAVANA_CNA the same contigs file as SAVANA_RUN in paired mode
  
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  a0f6f1a
- Rejoin each small-variant arm to one record per position before phasing
  
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  3858c1f
- Initialise the ClairS-TO PoN lists and omit the PoN flags when none resolve
  
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  cf49d47
- Stop PREPARE_AA_DATA_REPO reading a versions emit UNTAR does not have; test the download branch
  
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  0dc1303
- Download the SigProfiler genome by default; a given --sigprofiler_genome_dir still wins
  
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  9d704a1
- Skip CoRAL and signatures in test_full and carry over the chr19 SAVANA workarounds
  
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  fdba1b9
- Ignore, rather than fail, a CoRAL task that is still killed after its last retry
  
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  fd217ed
- Treat a missing SBS96 matrix as optional so zero-SNV samples reach the signature fit
  
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  eb72c5e
- Write ASCAT segments to CoRAL as 0-based BED tiling each contig without gaps
  
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  8178c15
- Reserve one solver thread for SCIP, which is single-threaded
  
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  5c523cc
- Decompose cycles once: skip it in reconstruct under --coral_run_cycle, else pass the alpha
  
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  4da8a2a
- Validate --germline_var_keep and --somatic_var_keep at launch
  
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  a3fb8dd
- Publish CORAL_CYCLE's cycles dir at ecdna/coral/cycles, not cycles/cycles
  
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  30a7798
- Drop the genome's default AA data repo MD5 when --aa_data_repo_url overrides the URL
  
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  cbccb7b
- Name CoRAL's summary <prefix>_amplicon_summary.txt in globs and stubs, as CoRAL writes it
  
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  e437376
- Drop CoRAL's Pyomo models/ dumps before the reconstruction and cycles dirs are published
  
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  0b12213
- Fail at launch under conda when modkit, the report or signatures would run
  
  robert-a-forsyth
  and
  claude
  committed
  fecfe14
- Drop ClairS-TO germline calls that fail another filter when the PASS filter is on
  
  robert-a-forsyth
  and
  claude
  committed
  75cfca3
- Report AlphaMissenseProtein aa_mismatch only for a reference-residue disagreement at the exact position
  
  robert-a-forsyth
  and
  claude
  committed
  d2cbb06
- Retry-then-ignore AmpliconClassifier failures and declare the outputs it writes beyond the core set
  
  robert-a-forsyth
  and
  claude
  committed
  e340727
- Give the skip_ampliconclassifier ECDNA test a real repo, so the param is what blocks AC
  
  robert-a-forsyth
  and
  claude
  committed
  648d045
- Document the AlphaMissenseProtein table format and the SAVANA VEP output; drop the WhatsHap-in-report claim
  
  robert-a-forsyth
  and
  claude
  committed
  9f48b1e
- PASS-filter tumour-only DeepVariant germline calls when no DeepSomatic verdict applies
  
  robert-a-forsyth
  and
  claude
  committed
  e62e5a7
- Document CoRAL's amplicon summary name, the cycles dir and per-process Gurobi maxForks
  
  robert-a-forsyth
  and
  claude
  committed
  ddf53d0
- Strip only the NanoStats _aln suffix in MultiQC instead of truncating at any _aln
  
  robert-a-forsyth
  and
  claude
  committed
  ce8718a
- Remove linting_comment.yml, which pr-comment.yml replaces in the 4.1.0 template
  
  robert-a-forsyth
  and
  claude
  committed
  05b3e49
- Restore the empty notes column on lymphoid panel rows and keep pre-commit from stripping it
  
  robert-a-forsyth
  and
  claude
  committed
  56dca7d
- Correct the wget CA-bundle comment: the image ships one and verification works
  
  robert-a-forsyth
  and
  claude
  committed
  9cc4917
- Merge ecDNA/CoRAL review fixes into coral
  robert-a-forsyth
  committed
  46ed6f9
- Merge wiring/config review fixes into coral
  robert-a-forsyth
  committed
  92a359a
- Declare aa_data_repo_url as a hidden schema param
  
  robert-a-forsyth
  and
  claude
  committed
  e93af8d
- Carry multi-valued DeepSomatic FILTERs into INFO/DS_VERDICT comma-separated
  
  robert-a-forsyth
  and
  claude
  committed
  4cdc2b0
- Make PhasedVcf.isAlt null-safe for records without GT
  
  robert-a-forsyth
  and
  claude
  committed
  e68dce3
- Document the tumour-only germline PASS rules, the per-caller union dedup and the pre-phasing rejoin
  
  robert-a-forsyth
  and
  claude
  committed
  a03ba35
- Regenerate snapshots after merging dev
  
  ljwharbers
  and
  claude
  committed
  f74b247
- Merge small-variant review fixes into coral
  robert-a-forsyth
  committed
  f797f60
- Changelog the coral review fixes
  
  robert-a-forsyth
  and
  claude
  committed
  d803223
- Move SigProfiler to the corrected CHM13-T2T payload (SPMG 7894689)
  
  ljwharbers
  and
  claude
  committed
  d86d968
- Fill in PR number in CHANGELOG entry
  ljwharbers
  committed
  f7a45c4
- Verify user-supplied SigProfiler volumes up front; cover GRCh38 too
  
  ljwharbers
  and
  claude
  committed
  1d3b7c7
- Name the cause in SIGPROFILER_VERIFY errors; stub-test the signatures chain
  
  ljwharbers
  and
  claude
  committed
  f20a2a2
- Merge pull request #216 from IntGenomicsLab/fix/sigprofiler-chm13-payload
  ljwharbers
  authored
  b9e6800
- Merge branch 'dev' into chore/module-updates
  
  ljwharbers
  and
  claude
  committed
  e5284ea
- Regenerate clair_only, default and consensus snapshots for the review fixes
  
  robert-a-forsyth
  and
  claude
  committed
  ca6a5ba
- Merge pull request #212 from IntGenomicsLab/chore/module-updates
  AmberVerhasselt
  authored
  f590906
- Expose SAVANA BEDPE, purity/ploidy and allele counts for downstream annotation
  
  Tim-Yu
  and
  claude
  committed
  382b4be
- Add Padfoot annotation and ReConPlot figures on top of the SAVANA subworkflows
  
  Tim-Yu
  and
  claude
  committed
  b0caeb0
- Document Padfoot and ReConPlot across README, CITATIONS, CHANGELOG and docs
  
  Tim-Yu
  and
  claude
  committed
  cad01d9
- Move the Padfoot and ReConPlot wiring into local subworkflows
  
  Tim-Yu
  and
  claude
  committed
  301bcb8
- Ship the ReConPlot wrapper under assets/ instead of downloading it at run time
  
  Tim-Yu
  and
  claude
  committed
  db09218
- Name ReConPlot caller-pair folders SV caller first, matching Padfoot
  
  Tim-Yu
  and
  claude
  committed
  5fd3ef2
- Add stub nf-tests for the Padfoot and ReConPlot subworkflows
  
  Tim-Yu
  and
  claude
  committed
  dd2e5c0
- Bring the Padfoot and ReConPlot docs in line with dev's conventions
  
  Tim-Yu
  and
  claude
  committed
  bc0ff52
- Update usage instructions for VEP plugins
  
  Tim-Yu
  and
  Copilot
  committed
  bd858a5
- Point the CHANGELOG entries at PR #202
  Tim-Yu
  committed
  8ba81b4
- Ship Padfoot and the ReConPlot package inside their images, drop the run-time downloads
  
  Tim-Yu
  and
  claude
  committed
  d29b27a
- Assert on the files each stub task receives, and cover ASCAT + Severus for tumour-only samples
  
  Tim-Yu
  and
  claude
  committed
  f0e9b67
- Make the two known ReConPlot failure modes warn-and-continue, validate --reconplot_regions at start-up
  
  Tim-Yu
  and
  claude
  committed
  5332502
- Share the Padfoot genome gate between the workflow and the parameter validator
  
  Tim-Yu
  and
  claude
  committed
  d42f18f
- Restore the second collapsed admonition in docs/usage.md and realign the option tables
  
  Tim-Yu
  and
  claude
  committed
  bdc3b72
- Drop the Go-template example from the Padfoot container README
  
  Tim-Yu
  and
  claude
  committed
  f04d3b8
- Address the automated review: run the module tests in PR CI, add help_text to every new parameter, fix two doc leftovers
  
  Tim-Yu
  and
  claude
  committed
  26e2c32
- Use the singularity/docker container ternary for PADFOOT and RECONPLOT with prebuilt SIF twins
  
  Tim-Yu
  and
  claude
  committed
  5b87b18
- Run PADFOOT and RECONPLOT for real in CI on synthetic fixtures
  
  Tim-Yu
  and
  claude
  committed
  962c3f5
- Harden the ReConPlot wrapper: stable tables, no aborts on odd records, consistent filters
  
  Tim-Yu
  and
  claude
  committed
  d2dc551
- Guard the Padfoot/ReConPlot configuration: species name, quoting, validation, skip under conda
  
  Tim-Yu
  and
  claude
  committed
  fd878b3
- Move the Padfoot and ReConPlot images to Docker Hub, fix the ReConPlot genome-wide clipping, label copy number against the tumour ploidy
  
  Tim-Yu
  and
  claude
  committed
  57c5af0
- Docs and metadata follow-ups from the review
  
  Tim-Yu
  and
  claude
  committed
  4536872
- Fold SEVERUS_WHITELIST into SEVERUS (optional whitelist input)
  
  AmberVerhasselt
  and
  claude
  committed
  38e5191
- Address review on #215: meta.yml inputs, module tests, small whitelist test
  
  AmberVerhasselt
  and
  claude
  committed
  9016b74
- Move SEVERUS whitelist test to tests/modules to satisfy nf-core lint
  
  AmberVerhasselt
  and
  claude
  committed
  ce36b24
Commits on Oct 3, 2026
- fix: make VEPPLUGIN tabix version eval work with BusyBox grep
  
  laulambr
  and
  claude
  committed
  b7425a3
- docs: changelog entry for VEPPLUGIN tabix version fix
  
  laulambr
  and
  claude
  committed
  3daa2a2
Commits on Oct 5, 2026
- Use Padfoot 3846215: correct breakpoint-to-gene lookup, exon/intron labels and known-fusion detection
  
  Tim-Yu
  and
  claude
  committed
  44e4c95
- Keep the ReConPlot figures a task could draw, and skip ASCAT pairs without a solution
  
  Tim-Yu
  and
  claude
  committed
  bc9ae54
- Merge branch 'dev' into coral
  robert-a-forsyth
  authored
  328eb28
- Read Wakhan 0.5.0's ranked solutions in Padfoot and ReConPlot
  
  Tim-Yu
  and
  claude
  committed
  9998450
- Retry resource kills before ignoring, fix the mm10 species, keep SAVANA figures without SVs, check --padfoot_genome
  
  Tim-Yu
  and
  claude
  committed
  8211aa2
- Merge origin/coral (dev merge) into local coral
  
  robert-a-forsyth
  and
  claude
  committed
  4c486ff
- Use Padfoot 1748e84: custom annotations, quoted commands, breakpoint repeats, robust Wakhan input
  
  Tim-Yu
  and
  claude
  committed
  03756c8
- Act on the second independent review: valid stub versions, Dfam outside /home, non-fatal focus panel, cache and gate fixes
  
  Tim-Yu
  and
  claude
  committed
  cfa60a9
- Check the Padfoot and ReConPlot steps in the preview test's workflow graph
  
  Tim-Yu
  and
  claude
  committed
  d7c7008
- Satisfy pre-commit and nf-core lint for the new fixtures and preview test
  
  Tim-Yu
  and
  claude
  committed
  a735e01
Commits on Oct 6, 2026
- Regenerate snapshots after merging dev into coral
  
  robert-a-forsyth
  and
  claude
  committed
  7e303a4
- Drop genome-derived params from the schema and prettier-format docs
  
  robert-a-forsyth
  and
  claude
  committed
  6e4982e
- Stop publishing the downloaded Clair3 model to the results
  
  robert-a-forsyth
  and
  claude
  committed
  aa6c6cf
Commits on Oct 7, 2026
Commits on Oct 12, 2026
- Merge origin/dev into coral
  
  robert-a-forsyth
  and
  claude
  committed
  ea02a32
- Move fiber-seq into a FIBERSEQ subworkflow to fit the workflow size limit
  
  robert-a-forsyth
  and
  claude
  committed
  d56e7e8
- Update the tumour BAM md5s in the default pipeline snapshot
  
  robert-a-forsyth
  and
  claude
  committed
  fd2875b
- Give SAMTOOLS_MERGE 8 cpus
  
  robert-a-forsyth
  and
  claude
  committed
  813d4a6
Commits on Oct 13, 2026
- Merge pull request #205 from IntGenomicsLab/coral
  robert-a-forsyth
  authored
  91b8c1e
- Export per-mutation signature probabilities from SigProfilerAssignment
  
  robert-a-forsyth
  and
  claude
  committed
  46ed210

Commits

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Commits on Oct 1, 2026