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Add LRSOMATICREPORT as the final pipeline step - #176

Merged

ljwharbers merged 23 commits into

devfrom

worktree-lrsomatic-report-module

Sep 8, 2026

Merged

Add LRSOMATICREPORT as the final pipeline step#176
ljwharbers merged 23 commits into
devfrom
worktree-lrsomatic-report-module

Commits on Jun 3, 2026
- Merge pull request #161 from IntGenomicsLab/dev
  robert-a-forsyth
  authored
  bf9bbbf
Commits on Jul 15, 2026
- feat: add LRSOMATICREPORT as the final pipeline step
  
  ljwharbers
  and
  claude
  committed
  9af50f1
Commits on Jul 16, 2026
- fix: resolve five bugs blocking LRSOMATICREPORT CI (PR #176)
  
  ljwharbers
  and
  claude
  committed
  c802922
Commits on Jul 17, 2026
- fix: use docker-context Wave build for LRSOMATICREPORT container
  
  ljwharbers
  and
  claude
  committed
  f9c1d3d
- fix: replace stageInMode copy with explicit cp -rL for report_src
  
  ljwharbers
  and
  claude
  committed
  4df21e1
Commits on Aug 12, 2026
- feat: vendor lrsomatic_report v1.1.0 and wire the report to SV VEP + Wakhan
  
  ljwharbers
  and
  claude
  committed
  95bb782
- fix: exempt .gitattributes from the nf-core template-unchanged check
  
  ljwharbers
  and
  claude
  committed
  820bbf7
Commits on Aug 14, 2026
- Merge remote-tracking branch 'origin/dev' into worktree-lrsomatic-report-module
  ljwharbers
  committed
  2308cb9
- fix: stage the report gene panel and stop clobbering CONDA_PREFIX
  
  ljwharbers
  and
  claude
  committed
  d729fcf
Commits on Aug 28, 2026
- chore: re-sync the vendored lrsomatic_report to v1.2.1
  
  ljwharbers
  and
  claude
  committed
  60847fc
- Merge remote-tracking branch 'origin/dev' into worktree-lrsomatic-report-module
  ljwharbers
  committed
  21d6bdb
Commits on Sep 1, 2026
Commits on Sep 2, 2026
- fix(tests): stop snapshotting sample4's merged BAM md5
  
  ljwharbers
  and
  claude
  committed
  5a13513
- Merge pull request #186 from IntGenomicsLab/fix/lrsomaticreport-container-and-ascat-list
  ljwharbers
  authored
  ddfc4ea
- fix: address remaining PR #176 review comments
  
  ljwharbers
  and
  claude
  committed
  cdd98db
- Merge pull request #187 from IntGenomicsLab/fix/pr176-review-nits
  ljwharbers
  authored
  3d454bf
- chore: trim over-explained comments added by this PR
  
  ljwharbers
  and
  claude
  committed
  20ccd2a
Commits on Sep 3, 2026
- style: trim report-module comments in pipeline-owned files to one line
  
  ljwharbers
  and
  claude
  committed
  a1b8855
- chore: re-sync vendored lrsomatic_report to v1.3.2
  
  ljwharbers
  and
  claude
  committed
  45a59e6

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Add LRSOMATICREPORT as the final pipeline step - #176

Add LRSOMATICREPORT as the final pipeline step#176
ljwharbers merged 23 commits into
devfrom
worktree-lrsomatic-report-module

Commits on Jun 3, 2026

Merge pull request #161 from IntGenomicsLab/dev

Commits on Jul 15, 2026

feat: add LRSOMATICREPORT as the final pipeline step

Commits on Jul 16, 2026

fix: resolve five bugs blocking LRSOMATICREPORT CI (PR #176)

Commits on Jul 17, 2026

fix: use docker-context Wave build for LRSOMATICREPORT container

fix: replace stageInMode copy with explicit cp -rL for report_src

Commits on Aug 12, 2026

feat: vendor lrsomatic_report v1.1.0 and wire the report to SV VEP + Wakhan

fix: exempt .gitattributes from the nf-core template-unchanged check

Commits on Aug 14, 2026

Merge remote-tracking branch 'origin/dev' into worktree-lrsomatic-report-module

fix: stage the report gene panel and stop clobbering CONDA_PREFIX

Commits on Aug 28, 2026

chore: re-sync the vendored lrsomatic_report to v1.2.1

Merge remote-tracking branch 'origin/dev' into worktree-lrsomatic-report-module

Commits on Sep 1, 2026

fix(lrsomaticreport): drop task.ext reference from container directive

fix(lrsomatic): flatten ch_ascat_files before it reaches LRSOMATICREPORT

Remove explanatory comments from container and ascat fixes

Merge pull request #185 from IntGenomicsLab/fix/lrsomaticreport-container-and-ascat-list

feat: apply several report gene panels at once

Commits on Sep 2, 2026

fix(tests): stop snapshotting sample4's merged BAM md5

Merge pull request #186 from IntGenomicsLab/fix/lrsomaticreport-container-and-ascat-list

fix: address remaining PR #176 review comments

Merge pull request #187 from IntGenomicsLab/fix/pr176-review-nits

chore: trim over-explained comments added by this PR

Commits on Sep 3, 2026

style: trim report-module comments in pipeline-owned files to one line

chore: re-sync vendored lrsomatic_report to v1.3.2