Add scout support for tomte

[fevac]

Description

Added

• Scout config creation and upload for tomte

Changed

• Updated delivery report for tomte to include information about which files are uploaded to Scout

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 add_scout_for_tomte -a

How to test

• Store case and generate report if not done already,cg workflow tomte store legalpeacock; cg generate delivery-report legalpeacock -f . Make sure delivery type is set to scout.
• cg upload -c legalpeacock -r . Make sure the upload is successful
• The scout_load.yaml should look like this:

---
analysis_date: 2024-08-07 10:05:18
default_gene_panels: []
delivery_report: /home/proj/stage/housekeeper-bundles/legalpeacock/2024-08-07/delivery-report.html
family: legalpeacock
family_name: XXXX-RNA-5M_downsampled
gene_panels:
- BRAIN
- Cardiology
- CILM
- CH
- CTD
- DIAB
- ENDO
- EP
- HEARING
- HYDRO
- IBMFS
- IEM
- IF
- mcarta
- MHT
- MIT
- MOVE
- mtDNA
- NBS-M
- NEURODEG
- NMD
- OMIM-AUTO
- OPTIC
- PANELAPP-GREEN
- PEDHEP
- PID
- PIDCAD
- RETINA
- SKD
- SOVM
- STROKE
- AID
- Inherited cancer
human_genome_build: '38'
multiqc_rna: /home/proj/stage/housekeeper-bundles/legalpeacock/2024-08-07/multiqc_report.html
omics_files:
  fraser: /home/proj/stage/housekeeper-bundles/legalpeacock/2024-08-07/legalpeacock_fraser_top_hits_clinical.tsv
  outrider: /home/proj/stage/housekeeper-bundles/legalpeacock/2024-08-07/legalpeacock_outrider_top_hits_clinical.tsv
owner: cust000
samples:
- analysis_type: wts
  father: '0'
  mother: '0'
  phenotype: unknown
  rna_alignment_path: /home/proj/stage/housekeeper-bundles/legalpeacock/2024-08-07/ACC9480A3DS5C0M.cram
  rna_coverage_bigwig: /home/proj/stage/housekeeper-bundles/legalpeacock/2024-08-07/ACC9480A3DS5C0M.bw
  sample_id: ACC9480A3DS5C0M
  sample_name: ACC9480A3DS5C0M
  sex: male
  splice_junctions_bed: /home/proj/stage/housekeeper-bundles/legalpeacock/2024-08-07/ACC9480A3DS5C0M_junction.bed.gz
  tissue_type: unknown
track: rare
vcf_snv: /home/proj/stage/housekeeper-bundles/legalpeacock/2024-08-07/legalpeacock_vep_clinical.vcf.gz
vcf_snv_research: /home/proj/stage/housekeeper-bundles/legalpeacock/2024-08-07/legalpeacock_vep_research.vcf.gz

• Scout contains Clinical WTS outliers

• Test scout upload for a case for which DROP was not run. scout_load.yaml should contain omics_files: {} and Scout should not show the outliers table.

• Delivery report is updated to include information about files uploaded to Scout

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 ...

[fevac]

tests are passing

[diitaz93]

Looks great ⭐ Can't say much about the RNA flow unfortunately, as I lack the knowledge, but the implementation looks super clean

[ivadym]

Nice! Looks great! 💯

[henrikstranneheim]

Nice!

[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

[fevac]

To include once this is PR ready: Clinical-Genomics/scout#4654

• fraser_tsv
• outrider_tsv

[ivadym]

Fantastic work 💯 🌟

[fevac]

@jemten @rannick this PR is ready and reviewed. Whenever ready to be put in production just merge master and you should be good to go

[fevac]

Tests were done with genomic-medicine-sweden/tomte: v2.0.1-ge68af17

[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

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

See analysis details on SonarCloud

[rannick]

I am going to close this PR for now as we went for the mip-rna approach of loading rna case to the related dna ones. This should be reopened/something similar should be done when we will homogenize scout loading with config files for all workflows