add nallo cg workflow config-case

[peterpru]

Description

Add nallo config-case. This generates 3 files needed to start the analysis in nextflow.

For the reviewer: this is the same as for raredisease, except for three things.

1. For nallo we need bam file paths as input for the sample sheet instead of fastq files. In this PR the bam file paths are collected from housekeeper.
2. For the nallo pipeline we need the sample sheet to have maximum one bam file per line. Instead of having having one sample per line in the samplsheet, we can have multiple. Here the all bam file paths are collected, and for each bam file entry, it will create a sample entry in the sample sheet.
3. no resolve-decompression. Input is bamfiles, so we can skip the entire spring->fastq checking and decompressing.

Added

• cg workflow nallo config-case

Changed

Fixed

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-nallo-config-case

How to test

• Do cg workflow nallo config-case rightalpaca

Expected test outcome

• The command should create a rightalpaca_samplesheet.csv, params file and config.yaml
• Files should have content, where params and config are populated from servers, and samplesheet from cg.
• 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 ...

[Vince-janv]

Nice 👍

[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

[peterpru]

Thanks for the review @Vince-janv

Deployed in stage:

Deployed in production: