Mention the clinical snv file in the Raredisease delivery report

[islean]

Description

Closes #5290. Turns out that the tag used to fetch the clinical snv file from housekeeper is also used for the mitochondrial snv file. Since the latter is created at a later date, it is always the one mentioned in the delivery report. This PR makes sure both files are fetched from HK.

Added

Changed

Fixed

• Both the mitochondrial and regular clinical snv files are shown in the Raredisease delivery report.

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 mt-snv-delivery-report -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 ...

[islean]

Tested on stage:

          <!-- Uploaded files -->
          


<div class="container mb-5">
  <h3 class="mb-4">Uppladdade filer</h3>
  <div class="alert alert-info" role="alert">
    Ytterligare information om de specifika levererade filerna finns på:
    <a href="****" class="alert-link">
      ****</a>.
  </div>
  <!-- Scout files -->
  


<h4 class="mt-4 mb-3">Scout</h4>
<div class="alert alert-info" role="alert">
  Varianter finns uppladdade i Scout:
  
  <a href="https://scout38.sys.scilifelab.se/****/****" class="alert-link">
    https://scout38.sys.scilifelab.se/****/****</a>.
  
</div>

<!-- Raredisease Scout files -->

<table class="table w-auto align-middle" aria-describedby="raredisease-scout-table">
  <tbody>
    
    <tr>
      <th scope="row">Kliniskt relevanta SNVs och INDELs</th>
      <td><case_name>_snv_ranked_clinical.vcf.gz</td>
      <td><case_name>_mt_ranked_clinical.vcf.gz</td>
    </tr>
      
    <tr>
      <th scope="row">Kliniskt relevanta SVs</th>
      <td><case_name>_sv_ranked_clinical.vcf.gz</td>
    </tr>
      
    <tr>
      <th scope="row">Kliniskt relevanta STRs</th>
      <td><case_name>_repeat_expansion_stranger.vcf.gz</td>
    </tr>
     
    <tr>
      <th scope="row">SMN CNVs</th>
      <td><case_name>_smncopynumbercaller.tsv</td>
    </tr>
    
  </tbody>
</table>

[sonarqubecloud]

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

[diitaz93]

Looks great 💯

[islean]

Deployed to Hasta:

INFO  [alembic.runtime.migration] Context impl MySQLImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
repository is clean
Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... done.
Log deploy... done.
cg, version 88.7.5
[isak.ohlsson@hasta:~] [P_base] $