add manifest to all nextfow pipelines

[rannick]

Description

Added

• Storing of a manifest.json file for all nextflow-based pipelines

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 [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 ...

[diitaz93]

👍

[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 SonarCloud

[rannick]

Getting version of deploy scripts... /home/hiseq.clinical
done.
Log deploy... done.
cg, version 62.2.16
remote: Enumerating objects: 1339, done.
remote: Counting objects: 100% (1040/1040), done.
remote: Compressing objects: 100% (308/308), done.
remote: Total 1339 (delta 854), reused 856 (delta 731), pack-reused 299 (from 1)
Receiving objects: 100% (1339/1339), 375.45 KiB | 0 bytes/s, done.
Resolving deltas: 100% (969/969), completed with 124 local objects.
From https://github.com/Clinical-Genomics/cg
   8823a1d..8901c8d  master     -> origin/master
 * [new branch]      575-add-get-related-dna-cases-from-rna-case -> origin/575-add-get-related-dna-cases-from-rna-case
 * [new branch]      add-microbial-order -> origin/add-microbial-order
 * [new branch]      add-questions-to-template -> origin/add-questions-to-template
   5e36cac..9be8693  add-raredisease-pedigree-check -> origin/add-raredisease-pedigree-check
   6de4df9..ea53580  add-raredisease-scout-upload -> origin/add-raredisease-scout-upload
 * [new branch]      add_well_position_validation -> origin/add_well_position_validation
   3290091..e2e4ee5  dev-new-delivery-service -> origin/dev-new-delivery-service
 * [new branch]      managed_variants_in_params -> origin/managed_variants_in_params
   bc15b03..08ceb20  patch_taxprofiler_versions -> origin/patch_taxprofiler_versions
   3c6742b..61a5f91  refactor-fastq-workflow -> origin/refactor-fastq-workflow
   74160c7..7913bfc  rename-order-status-column -> origin/rename-order-status-column
 * [new tag]         v62.2.16   -> v62.2.16
From https://github.com/Clinical-Genomics/cg
 * [new tag]         v62.2.14   -> v62.2.14
 * [new tag]         v62.2.15   -> v62.2.15
Already on 'master'
Your branch is behind 'origin/master' by 6 commits, and can be fast-forwarded.
  (use "git pull" to update your local branch)
Updating 8823a1d..8901c8d
Fast-forward
 .bumpversion.cfg                                  |   2 +-
 Dockerfile                                        |   1 -
 cg/__init__.py                                    |   2 +-
 cg/apps/invoice/templates/KI_pool_invoice.xlsx    | Bin 113467 -> 113533 bytes
 cg/apps/invoice/templates/KI_sample_invoice.xlsx  | Bin 75562 -> 75147 bytes
 cg/apps/invoice/templates/KTH_pool_invoice.xlsx   | Bin 113512 -> 113053 bytes
 cg/apps/invoice/templates/KTH_sample_invoice.xlsx | Bin 75459 -> 75008 bytes
 cg/resources/raredisease_bundle_filenames.yaml    |   6 ++++++
 cg/resources/rnafusion_bundle_filenames.yaml      |   6 ++++++
 cg/resources/taxprofiler_bundle_filenames.yaml    |   8 ++++++--
 cg/resources/tomte_bundle_filenames.yaml          |   6 ++++++
 pyproject.toml                                    |   2 +-
 templates/config.yaml                             |  32 --------------------------------
 13 files changed, 27 insertions(+), 38 deletions(-)
 delete mode 100644 templates/config.yaml
/home/hiseq.clinical
INFO  [alembic.runtime.migration] Context impl MySQLImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.