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Feat(Nallo) Add Methbat files and update modkit #157

Merged
inemesb merged 3 commits intomainfrom
nallo-methbat
Jan 28, 2026
Merged

Feat(Nallo) Add Methbat files and update modkit #157
inemesb merged 3 commits intomainfrom
nallo-methbat

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@inemesb
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@inemesb inemesb commented Jan 23, 2026

Description

Added

  • methbat bed files
  • methbat profile tsv file

Changed

  • modkit bed file tags
  • made modkit files optional

Testing

How to prepare for test

  • ssh to Hasta
  • Test your branch with
hermes-test-deploy <branch-name>
hermes-test <command here>

How to test

  • login to ...
  • do ...

Expected test result

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

Review

  • code approved by
  • 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

@codecov-commenter
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codecov-commenter commented Jan 23, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.81%. Comparing base (30521a8) to head (54aa37e).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #157      +/-   ##
==========================================
+ Coverage   92.78%   92.81%   +0.02%     
==========================================
  Files          28       28              
  Lines        1012     1016       +4     
==========================================
+ Hits          939      943       +4     
  Misses         73       73              
Flag Coverage Δ
unittests 92.81% <100.00%> (+0.02%) ⬆️

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@inemesb
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inemesb commented Jan 23, 2026

Stored successfully with Clinical-Genomics/cg#4852.

linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A5DS70GB/ACC17426A5DS70GB_pbcpgtools.hap1.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/ACC17426A5DS70GB_methbat_profile.tsv

linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A1DS70GB/ACC17426A1DS70GB_pbcpgtools.hap1.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A1DS70GB_pbcpgtools.hap1.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A1DS70GB/ACC17426A1DS70GB_pbcpgtools.hap1.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A1DS70GB_pbcpgtools.hap1.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A1DS70GB/ACC17426A1DS70GB_pbcpgtools.hap2.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A1DS70GB_pbcpgtools.hap2.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A1DS70GB/ACC17426A1DS70GB_pbcpgtools.hap2.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A1DS70GB_pbcpgtools.hap2.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A1DS70GB/ACC17426A1DS70GB_pbcpgtools.combined.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A1DS70GB_pbcpgtools.combined.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A1DS70GB/ACC17426A1DS70GB_pbcpgtools.combined.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A1DS70GB_pbcpgtools.combined.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/profile/ACC17426A1DS70GB/ACC17426A1DS70GB_methbat_profile.tsv -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A1DS70GB_methbat_profile.tsv

linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_pbcpgtools.hap1.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB_pbcpgtools.hap1.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_pbcpgtools.hap1.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB_pbcpgtools.hap1.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_pbcpgtools.hap2.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/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/2026-01-23/ACC17426A3DS70GB_pbcpgtools.hap2.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_pbcpgtools.combined.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB_pbcpgtools.combined.bed.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_pbcpgtools.combined.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB_pbcpgtools.combined.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/profile/ACC17426A3DS70GB/ACC17426A3DS70GB_methbat_profile.tsv -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB_methbat_profile.tsv
Full output
[ine.esbensen@hasta:~] [S_base] $ cg workflow nallo store 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/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/2026-01-23
linked file: /home/proj/stage/analysis/cases/charmedswan/aligned_reads/ACC17426A1DS70GB/ACC17426A1DS70GB_haplotagged.bam -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A1DS70GB_haplotagged.bam
linked file: /home/proj/stage/analysis/cases/charmedswan/aligned_reads/ACC17426A1DS70GB/ACC17426A1DS70GB_haplotagged.bam.bai -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A1DS70GB_haplotagged.bam.bai
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A1DS70GB/ACC17426A1DS70GB_chromograph_coverage_chr1.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/ACC17426A1DS70GB_chromograph_autozyg_chr4.png
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linked file: /home/proj/stage/analysis/cases/charmedswan/svs/family/charmedswan/charmedswan_svs_annotated_ranked_research.vcf.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/charmedswan_svs_annotated_ranked_research.vcf.gz.tbi
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linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A3DS70GB/ACC17426A3DS70GB_chromograph_autozyg_chr21.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB_chromograph_autozyg_chr21.png
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linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A3DS70GB/ACC17426A3DS70GB_chromograph_autozyg_chrY.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB_chromograph_autozyg_chrY.png
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linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_pbcpgtools.hap1.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB_pbcpgtools.hap1.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_pbcpgtools.hap2.bed.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/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/2026-01-23/ACC17426A3DS70GB_pbcpgtools.hap2.bed.gz.tbi
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linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/pileup/ACC17426A3DS70GB/ACC17426A3DS70GB_pbcpgtools.combined.bed.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB_pbcpgtools.combined.bed.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/methylation/profile/ACC17426A3DS70GB/ACC17426A3DS70GB_methbat_profile.tsv -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB_methbat_profile.tsv
linked file: /home/proj/stage/analysis/cases/charmedswan/qc/mosdepth/ACC17426A3DS70GB/ACC17426A3DS70GB.per-base.d4 -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB.per-base.d4
linked file: /home/proj/stage/analysis/cases/charmedswan/qc/deepvariant_vcfstatsreport/ACC17426A3DS70GB/ACC17426A3DS70GB.visual_report.html -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB.visual_report.html
linked file: /home/proj/stage/analysis/cases/charmedswan/paraphase/sample/ACC17426A3DS70GB/ACC17426A3DS70GB.paraphase.bam -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB.paraphase.bam
linked file: /home/proj/stage/analysis/cases/charmedswan/paraphase/sample/ACC17426A3DS70GB/ACC17426A3DS70GB.paraphase.bam.bai -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/ACC17426A3DS70GB_hificnv.maf.bw
linked file: /home/proj/stage/analysis/cases/charmedswan/qc/phasing_stats/ACC17426A3DS70GB/ACC17426A3DS70GB_stats.blocks.gtf.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB_stats.blocks.gtf.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/qc/phasing_stats/ACC17426A3DS70GB/ACC17426A3DS70GB_stats.blocks.gtf.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A3DS70GB_stats.blocks.gtf.gz.tbi
linked file: /home/proj/stage/analysis/cases/charmedswan/aligned_reads/ACC17426A5DS70GB/ACC17426A5DS70GB_haplotagged.bam -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB_haplotagged.bam
linked file: /home/proj/stage/analysis/cases/charmedswan/aligned_reads/ACC17426A5DS70GB/ACC17426A5DS70GB_haplotagged.bam.bai -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB_haplotagged.bam.bai
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr1.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/ACC17426A5DS70GB_chromograph_coverage_chr4.png
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linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr9.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/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/2026-01-23/ACC17426A5DS70GB_chromograph_coverage_chr10.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr11.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB_chromograph_coverage_chr11.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr12.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/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/2026-01-23/ACC17426A5DS70GB_chromograph_coverage_chr13.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr14.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB_chromograph_coverage_chr14.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr15.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB_chromograph_coverage_chr15.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr16.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB_chromograph_coverage_chr16.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr17.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB_chromograph_coverage_chr17.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr18.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB_chromograph_coverage_chr18.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr19.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB_chromograph_coverage_chr19.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr20.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB_chromograph_coverage_chr20.png
linked file: /home/proj/stage/analysis/cases/charmedswan/images/chromograph/sample/ACC17426A5DS70GB/ACC17426A5DS70GB_chromograph_coverage_chr21.png -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/ACC17426A5DS70GB.visual_report.html
linked file: /home/proj/stage/analysis/cases/charmedswan/paraphase/sample/ACC17426A5DS70GB/ACC17426A5DS70GB.paraphase.bam -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB.paraphase.bam
linked file: /home/proj/stage/analysis/cases/charmedswan/paraphase/sample/ACC17426A5DS70GB/ACC17426A5DS70GB.paraphase.bam.bai -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/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/2026-01-23/ACC17426A5DS70GB_hificnv.maf.bw
linked file: /home/proj/stage/analysis/cases/charmedswan/qc/phasing_stats/ACC17426A5DS70GB/ACC17426A5DS70GB_stats.blocks.gtf.gz -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB_stats.blocks.gtf.gz
linked file: /home/proj/stage/analysis/cases/charmedswan/qc/phasing_stats/ACC17426A5DS70GB/ACC17426A5DS70GB_stats.blocks.gtf.gz.tbi -> /home/proj/stage/housekeeper-bundles/charmedswan/2026-01-23/ACC17426A5DS70GB_stats.blocks.gtf.gz.tbi
Analysis successfully stored in Housekeeper: charmedswan (2026-01-23 14:54:30)
Marking analysis as completed in StatusDB for charmedswan
Action 'None' set for case charmedswan

@inemesb inemesb marked this pull request as ready for review January 26, 2026 08:27
@inemesb inemesb requested a review from a team as a code owner January 26, 2026 08:27
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Looks good!

@inemesb inemesb merged commit 7892e36 into main Jan 28, 2026
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@inemesb inemesb deleted the nallo-methbat branch January 28, 2026 12:38
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inemesb commented Jan 28, 2026

Deployed to production:

[ine.esbensen@hasta:~] [base] $ hermes-deploy
Are you sure you want to pull the latest Hermes image? [Y/n] y
Pulling the latest Hermes image which will be used in stage and prod
WARNING: Authentication token file not found : Only pulls of public images will succeed
INFO:    Starting build...
Getting image source signatures
Skipping fetch of repeat blob sha256:ccaf924377f936af2c0396fce237145b7d1ecc0b8196916667fc6d5ff4866e2d
Skipping fetch of repeat blob sha256:63c1c7b8e58b0b95a2f190ebf18f3c2573efb86c53db7f44be0c612f22ad9dfd
Skipping fetch of repeat blob sha256:1a204cbad1a24c09b543a5f1c57c6a21c3237e64648f279b76428ee90efb1e15
Skipping fetch of repeat blob sha256:273839f2f1f9c0824ce4929e13edabe329673e88266f2d07b5bc349014d526be
Copying blob sha256:035b156389b987f853505208ff99b054c88668bacbb7d95d633e84948e256fb3
 93 B / 93 B [==============================================================] 0s
Copying blob sha256:36ba30a010ceac9b9c3d9afbc83861e7aa788b522fcbb4ae6a1102e3e59afb41
 217.20 KiB / 217.20 KiB [==================================================] 0s
Copying blob sha256:b67e5f86133d3c56576bad69ab350c10fc5375cca07c4aec5f428e530a26c515
 41.32 MiB / 41.32 MiB [====================================================] 0s
Copying config sha256:9aac37166907227e8dadde0971aa711c4f8afb2d4925f872b625ccb057b8464d
 6.32 KiB / 6.32 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: /home/proj/production/singularity_cache/hermes_temp.sif
Successfully pulled the latest Hermes image.
mv: try to overwrite ‘/home/proj/production/singularity_cache/hermes_latest.sif’, overriding mode 0750 (rwxr-x---)? y

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3 participants