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Update Nallo to 0.10.2#4868

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update-nallo-revision
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Update Nallo to 0.10.2#4868
fellen31 wants to merge 1 commit intomasterfrom
update-nallo-revision

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@fellen31 fellen31 commented Feb 3, 2026 •
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Description

Goes together with Clinical-Genomics/hermes#158.

Added

  • Save GENS files from Nallo

Changed

  • WhatHap stats blocks file name

How to prepare for test

  • Ssh to relevant server (depending on type of change)
  • Use stage: us
  • Paxa the environment: paxa
  • Install on stage (example for Hasta): 
    bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b [THIS-BRANCH-NAME] -a

How to test

  • Do ...

Expected test outcome

  • Check that ...
  • Take a screenshot and attach or copy/paste the output.

Review

  • Tests executed by
  • "Merge and deploy" approved by
    Thanks for filling in who performed the code review and the test!

This version is a

  • MAJOR - when you make incompatible API changes
  • MINOR - when you add functionality in a backwards compatible manner
  • PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

  • Document in ...
  • Deploy this branch on ...
  • Inform to ...

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sonarqubecloud bot commented Feb 3, 2026

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

@fellen31 fellen31 changed the title Update Nallo to 0.10.0 Update Nallo to 0.10.1 Feb 5, 2026
@fellen31 fellen31 mentioned this pull request Feb 5, 2026
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@fellen31 fellen31 changed the title Update Nallo to 0.10.1 Update Nallo to 0.10.2 Feb 9, 2026
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fellen31 commented Feb 9, 2026

Testing:

[felix.lenner@hasta:~] [S_base] $ cg workflow nallo store charmedswan
Generating metrics file and performing QC checks for charmedswan
Case charmedswan exists in Status DB
Writing metrics deliverables file to /home/proj/stage/analysis/cases/charmedswan/charmedswan_metrics_deliverables.yaml
Validating QC metrics
Setting analysis status to completed for case charmedswan
Storing analysis for charmedswan
Case charmedswan exists in Status DB
Writing deliverables file in /home/proj/stage/analysis/cases/charmedswan/charmedswan_deliverables.yaml
Case charmedswan exists in Status DB
Storing bundle data in Housekeeper for charmedswan
Converting workflow deliverables to CG deliverables
Running command singularity run --bind /home/proj/stage:/home/proj/stage /home/proj/stage/singularity_cache/hermes_test.sif convert deliverables --workflow nallo /home/proj/stage/analysis/cases/charmedswan/charmedswan_deliverables.yaml
Optional file /home/proj/stage/analysis/cases/charmedswan/assembly/stats/ACC17426A1DS70GB/ACC17426A1DS70GB_haplotype_1.assembly_summary not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/assembly/stats/ACC17426A1DS70GB/ACC17426A1DS70GB_haplotype_2.assembly_summary not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/assembly/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_aligned_assembly.bam not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/assembly/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_aligned_assembly.bam.bai not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A1DS70GB/ACC17426A1DS70GB_modkit_pileup_1.bed.gz not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A1DS70GB/ACC17426A1DS70GB_modkit_pileup_1.bed.gz.tbi not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A1DS70GB/ACC17426A1DS70GB_modkit_pileup_2.bed.gz not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A1DS70GB/ACC17426A1DS70GB_modkit_pileup_2.bed.gz.tbi not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A1DS70GB/ACC17426A1DS70GB_modkit_pileup_ungrouped.bed.gz not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A1DS70GB/ACC17426A1DS70GB_modkit_pileup_ungrouped.bed.gz.tbi not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/manifest.json not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/assembly/stats/ACC17426A3DS70GB/ACC17426A3DS70GB_haplotype_1.assembly_summary not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/assembly/stats/ACC17426A3DS70GB/ACC17426A3DS70GB_haplotype_2.assembly_summary not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/assembly/sample/ACC17426A3DS70GB/ACC17426A3DS70GB_aligned_assembly.bam not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/assembly/sample/ACC17426A3DS70GB/ACC17426A3DS70GB_aligned_assembly.bam.bai not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_modkit_pileup_1.bed.gz not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_modkit_pileup_1.bed.gz.tbi not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_modkit_pileup_2.bed.gz not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_modkit_pileup_2.bed.gz.tbi not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_modkit_pileup_ungrouped.bed.gz not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_modkit_pileup_ungrouped.bed.gz.tbi not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/assembly/stats/ACC17426A5DS70GB/ACC17426A5DS70GB_haplotype_1.assembly_summary not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/assembly/stats/ACC17426A5DS70GB/ACC17426A5DS70GB_haplotype_2.assembly_summary not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/assembly/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_aligned_assembly.bam not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/assembly/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_aligned_assembly.bam.bai not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_modkit_pileup_1.bed.gz not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_modkit_pileup_1.bed.gz.tbi not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_modkit_pileup_2.bed.gz not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_modkit_pileup_2.bed.gz.tbi not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_modkit_pileup_ungrouped.bed.gz not found, removing from bundle.
Optional file /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_modkit_pileup_ungrouped.bed.gz.tbi not found, removing from bundle.
Use global root path /home/proj/stage/housekeeper-bundles
created new bundle version dir: /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09
linked file: /home/proj/stage/analysis/cases/charmedswan/aligned_reads/ACC17426A1DS70GB/ACC17426A1DS70GB_haplotagged.bam -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_haplotagged.bam
linked file: /home/proj/stage/analysis/cases/charmedswan/aligned_reads/ACC17426A1DS70GB/ACC17426A1DS70GB_haplotagged.bam.bai -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_haplotagged.bam.bai
linked file: /home/proj/stage/analysis/cases/charmedswan/gens/ACC17426A1DS70GB/ACC17426A1DS70GB.baf.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB.baf.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/gens/ACC17426A1DS70GB/ACC17426A1DS70GB.baf.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB.baf.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/gens/ACC17426A1DS70GB/ACC17426A1DS70GB.cov.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB.cov.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/gens/ACC17426A1DS70GB/ACC17426A1DS70GB.cov.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB.cov.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr1.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr1.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr2.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr2.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr3.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr3.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr4.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr4.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr5.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr5.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr6.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr6.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr7.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr7.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr8.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr8.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr9.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr9.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr10.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr10.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr11.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr11.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr12.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr12.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr13.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr13.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr14.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr14.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr15.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr15.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr16.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr16.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr17.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr17.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr18.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr18.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr19.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr19.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr20.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr20.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr21.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr21.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr22.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chr22.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chrX.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chrX.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chrY.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chrY.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chrM.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_coverage_chrM.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr1.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr1.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr2.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr2.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr3.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr3.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr4.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr4.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr5.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr5.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr6.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr6.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr7.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr7.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr8.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr8.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr9.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr9.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr10.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr10.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr11.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr11.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr12.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr12.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr13.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr13.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr14.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr14.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr15.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr15.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr16.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr16.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr17.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr17.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr18.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr18.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr19.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr19.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr20.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr20.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_autozyg_chr21.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A1DS70GB_chromograph_autozyg_chr21.png
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linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A3DS70GB/ACC17426A3DS70GB_chromograph_coverage_chr20.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_chromograph_coverage_chr20.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A3DS70GB/ACC17426A3DS70GB_chromograph_coverage_chr21.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_chromograph_coverage_chr21.png
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linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_pbcpgtools.hap2.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_pbcpgtools.hap2.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_pbcpgtools.hap2.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_pbcpgtools.hap2.bed.gz.tbi
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linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/profile/ACC17426A3DS70GB/ACC17426A3DS70GB_methbat_profile.tsv -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_methbat_profile.tsv
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linked file: /home/proj/stage/analysis/cases/charmedswan/paraphase/sample/ACC17426A3DS70GB/ACC17426A3DS70GB.paraphase.bam -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB.paraphase.bam
linked file: /home/proj/stage/analysis/cases/charmedswan/paraphase/sample/ACC17426A3DS70GB/ACC17426A3DS70GB.paraphase.bam.bai -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB.paraphase.bam.bai
linked file: /home/proj/stage/analysis/cases/charmedswan/repeats/sample/ACC17426A3DS70GB/ACC17426A3DS70GB_trgt.vcf.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_trgt.vcf.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/repeats/sample/ACC17426A3DS70GB/ACC17426A3DS70GB_trgt.vcf.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_trgt.vcf.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/repeats/sample/ACC17426A3DS70GB/ACC17426A3DS70GB_spanning_trgt.bam -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_spanning_trgt.bam
linked file: /home/proj/stage/analysis/cases/charmedswan/repeats/sample/ACC17426A3DS70GB/ACC17426A3DS70GB_spanning_trgt.bam.bai -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_spanning_trgt.bam.bai
linked file: /home/proj/stage/analysis/cases/charmedswan/visualization_tracks/ACC17426A3DS70GB/ACC17426A3DS70GB_hificnv.copynum.bedgraph -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_hificnv.copynum.bedgraph
linked file: /home/proj/stage/analysis/cases/charmedswan/visualization_tracks/ACC17426A3DS70GB/ACC17426A3DS70GB_hificnv.depth.bw -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_hificnv.depth.bw
linked file: /home/proj/stage/analysis/cases/charmedswan/visualization_tracks/ACC17426A3DS70GB/ACC17426A3DS70GB_hificnv.maf.bw -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_hificnv.maf.bw
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linked file: /home/proj/stage/analysis/cases/charmedswan/qc/phasing_stats/ACC17426A3DS70GB/ACC17426A3DS70GB_whatshap_stats.gtf.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A3DS70GB_whatshap_stats.gtf.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/aligned_reads/ACC17426A5DS70GB/ACC17426A5DS70GB_haplotagged.bam -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_haplotagged.bam
linked file: /home/proj/stage/analysis/cases/charmedswan/aligned_reads/ACC17426A5DS70GB/ACC17426A5DS70GB_haplotagged.bam.bai -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_haplotagged.bam.bai
linked file: /home/proj/stage/analysis/cases/charmedswan/gens/ACC17426A5DS70GB/ACC17426A5DS70GB.baf.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB.baf.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/gens/ACC17426A5DS70GB/ACC17426A5DS70GB.baf.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB.baf.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/gens/ACC17426A5DS70GB/ACC17426A5DS70GB.cov.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB.cov.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/gens/ACC17426A5DS70GB/ACC17426A5DS70GB.cov.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB.cov.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr1.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr1.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr2.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr2.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr3.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr3.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr4.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr4.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr5.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr5.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr6.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr6.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr7.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr7.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr8.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr8.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr9.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr9.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr10.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr10.png
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linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr12.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr12.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr13.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr13.png
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linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr21.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr21.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr22.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chr22.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chrX.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chrX.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chrY.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chrY.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chrM.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_coverage_chrM.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr1.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr1.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr2.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr2.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr3.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr3.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr4.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr4.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr5.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr5.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr6.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr6.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr7.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr7.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr8.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr8.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr9.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr9.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr10.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr10.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr11.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr11.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr12.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr12.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr13.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr13.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr14.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr14.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr15.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr15.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr16.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr16.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr17.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr17.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr18.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr18.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr19.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr19.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr20.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr20.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr21.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr21.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chr22.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chr22.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chrX.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chrX.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chrY.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chrY.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_autozyg_chrM.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_chromograph_autozyg_chrM.png
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_pbcpgtools.hap1.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_pbcpgtools.hap1.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_pbcpgtools.hap1.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_pbcpgtools.hap1.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_pbcpgtools.hap2.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_pbcpgtools.hap2.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_pbcpgtools.hap2.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_pbcpgtools.hap2.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_pbcpgtools.combined.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_pbcpgtools.combined.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_pbcpgtools.combined.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_pbcpgtools.combined.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/profile/ACC17426A5DS70GB/ACC17426A5DS70GB_methbat_profile.tsv -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_methbat_profile.tsv
linked file: /home/proj/stage/analysis/cases/charmedswan/qc/mosdepth/ACC17426A5DS70GB/ACC17426A5DS70GB.per-base.d4 -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB.per-base.d4
linked file: /home/proj/stage/analysis/cases/charmedswan/qc/deepvariant_vcfstatsreport/ACC17426A5DS70GB/ACC17426A5DS70GB.visual_report.html -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB.visual_report.html
linked file: /home/proj/stage/analysis/cases/charmedswan/paraphase/sample/ACC17426A5DS70GB/ACC17426A5DS70GB.paraphase.bam -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB.paraphase.bam
linked file: /home/proj/stage/analysis/cases/charmedswan/paraphase/sample/ACC17426A5DS70GB/ACC17426A5DS70GB.paraphase.bam.bai -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB.paraphase.bam.bai
linked file: /home/proj/stage/analysis/cases/charmedswan/repeats/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_trgt.vcf.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_trgt.vcf.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/repeats/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_trgt.vcf.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_trgt.vcf.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/repeats/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_spanning_trgt.bam -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_spanning_trgt.bam
linked file: /home/proj/stage/analysis/cases/charmedswan/repeats/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_spanning_trgt.bam.bai -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_spanning_trgt.bam.bai
linked file: /home/proj/stage/analysis/cases/charmedswan/visualization_tracks/ACC17426A5DS70GB/ACC17426A5DS70GB_hificnv.copynum.bedgraph -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_hificnv.copynum.bedgraph
linked file: /home/proj/stage/analysis/cases/charmedswan/visualization_tracks/ACC17426A5DS70GB/ACC17426A5DS70GB_hificnv.depth.bw -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_hificnv.depth.bw
linked file: /home/proj/stage/analysis/cases/charmedswan/visualization_tracks/ACC17426A5DS70GB/ACC17426A5DS70GB_hificnv.maf.bw -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_hificnv.maf.bw
linked file: /home/proj/stage/analysis/cases/charmedswan/qc/phasing_stats/ACC17426A5DS70GB/ACC17426A5DS70GB_whatshap_stats.gtf.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_whatshap_stats.gtf.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/qc/phasing_stats/ACC17426A5DS70GB/ACC17426A5DS70GB_whatshap_stats.gtf.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-02-09/ACC17426A5DS70GB_whatshap_stats.gtf.gz.tbi
Analysis successfully stored in Housekeeper: charmedswan (2026-02-09 09:05:49)
Marking analysis as completed in StatusDB for charmedswan
Action 'None' set for case charmedswan

@fellen31 fellen31 mentioned this pull request Feb 9, 2026
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@fellen31 fellen31 marked this pull request as ready for review February 10, 2026 09:36
@fellen31 fellen31 requested a review from a team as a code owner February 10, 2026 09:36
RasmusBurge-CG
RasmusBurge-CG approved these changes Feb 16, 2026
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Looks good to me!

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@RasmusBurge-CG RasmusBurge-CG RasmusBurge-CG approved these changes

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@fellen31 @RasmusBurge-CG