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Refactor pipeline to workflow #94

Merged
merged 8 commits into from
Feb 8, 2024
Merged

Refactor pipeline to workflow #94

merged 8 commits into from
Feb 8, 2024

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henrikstranneheim
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@henrikstranneheim henrikstranneheim commented Feb 6, 2024 •
edited
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Description

Changes

  • Refactor pipeline to workflow

How to prepare for test

  • ssh to hasta.scilifelab.se
  • 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_hermes -t hermes -b refactor-pipeline-to-workflow

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
  • Inform to ...

Linked to: Clinical-Genomics/cg#2911

@henrikstranneheim henrikstranneheim added the Enhancement New feature or request label Feb 6, 2024
@henrikstranneheim henrikstranneheim self-assigned this Feb 6, 2024
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codecov-commenter commented Feb 6, 2024 •
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Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (34d376a) 90.17% compared to head (32158ea) 90.16%.
Report is 1 commits behind head on main.

Files Patch % Lines
cg_hermes/cli/validate.py 92.30% 1 Missing ⚠️
cg_hermes/validate.py 83.33% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main      #94      +/-   ##
==========================================
- Coverage   90.17%   90.16%   -0.02%     
==========================================
  Files          25       25              
  Lines         560      559       -1     
==========================================
- Hits          505      504       -1     
  Misses         55       55
Flag Coverage Δ
unittests 90.16% <96.82%> (-0.02%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@henrikstranneheim
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cg workflow mutant store frankhusky 👍

 cg workflow mutant store frankhusky
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Called undefined __fields__ on HousekeeperAPI, please wrap
Case frankhusky exists in Status DB
Storing bundle data in Housekeeper for frankhusky
Converting workflow deliverables to CG deliverables
Running command /home/proj/stage/bin/miniconda3/envs/S_hermes/bin/hermes convert deliverables --workflow mutant /home/proj/stage/mutant/cases/frankhusky/results/frankhusky_deliverables.yaml
Use global root path /home/proj/stage/housekeeper-bundles
created new bundle version dir: /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19
linked file: /home/proj/stage/mutant/cases/frankhusky/results/instrument.properties -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/instrument.properties
linked file: /home/proj/stage/mutant/cases/frankhusky/results/sars-cov-2_395698_results.csv -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/sars-cov-2_395698_results.csv
linked file: /home/proj/stage/mutant/cases/frankhusky/results/sars-cov-2_395698_variants.csv -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/sars-cov-2_395698_variants.csv
linked file: /home/proj/stage/mutant/cases/frankhusky/results/395698.pangolin.csv -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698.pangolin.csv
linked file: /home/proj/stage/mutant/cases/frankhusky/results/395698_2024-01-19_pangolin_classification_format4.txt -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698_2024-01-19_pangolin_classification_format4.txt
linked file: /home/proj/stage/mutant/cases/frankhusky/results/395698.consensus.fa -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698.consensus.fa
linked file: /home/proj/stage/mutant/cases/frankhusky/results/395698_multiqc.html -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698_multiqc.html
linked file: /home/proj/stage/mutant/cases/frankhusky/results/395698_multiqc.json -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698_multiqc.json
linked file: /home/proj/stage/mutant/cases/frankhusky/results/nextclade_summary.csv -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/nextclade_summary.csv
linked file: /home/proj/stage/mutant/cases/frankhusky/results/frankhusky_metrics_deliverables.yaml -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/frankhusky_metrics_deliverables.yaml
linked file: /home/proj/stage/mutant/cases/frankhusky/case_config.json -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/case_config.json
linked file: /home/proj/stage/mutant/MUTANT/mutant/config/hasta/illumina_artic_v3.json -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/illumina_artic_v3.json
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_versions/frankhusky_240119-152718_versions.csv -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/frankhusky_240119-152718_versions.csv
linked file: /home/proj/stage/mutant/cases/frankhusky/results/nextflow.log -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/nextflow.log
linked file: /home/proj/stage/mutant/cases/frankhusky/results/395698_komplettering.csv -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/395698_komplettering.csv
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500657TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500657TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500657TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500657TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500657TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500657TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500657TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500657TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500658TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500658TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500658TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500658TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500658TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500658TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500658TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500658TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500659TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500659TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500659TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500659TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500659TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500659TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500659TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500659TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500660TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500660TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500660TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500660TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500660TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500660TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500660TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500660TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500661TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500661TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500661TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500661TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500661TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500661TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500661TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500661TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500662TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500662TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500662TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500662TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500662TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500662TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500662TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500662TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500663TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500663TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500663TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500663TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500663TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500663TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500663TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500663TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500664TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500664TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500664TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500664TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500664TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500664TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500664TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500664TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500665TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500665TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500665TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500665TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500665TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500665TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500665TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500665TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500666TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500666TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500666TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500666TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500666TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500666TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500666TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500666TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500667TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500667TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500667TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500667TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500667TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500667TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500667TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500667TEST.consensus.fasta
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500668TEST_1.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500668TEST_1.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/fastq/01_SE100_21CS500668TEST_2.fastq.gz -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500668TEST_2.fastq.gz
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_Genotyping_typeVariants/vcf/01_SE100_21CS500668TEST.vcf -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500668TEST.vcf
linked file: /home/proj/stage/mutant/cases/frankhusky/results/ncovIllumina_sequenceAnalysis_makeConsensus/01_SE100_21CS500668TEST.consensus.fasta -> /home/proj/stage/housekeeper-bundles/frankhusky/2024-01-19/01_SE100_21CS500668TEST.consensus.fasta
/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/apps/housekeeper/hk.py:325: SAWarning: Object of type <Version> not in session, add operation along 'Bundle.versions' will not proceed
  return self._store.session.commit()
/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/apps/housekeeper/hk.py:325: SAWarning: Object of type <File> not in session, add operation along 'Tag.files' won't proceed
  return self._store.session.commit()
Analysis successfully stored in Housekeeper: frankhusky : 2024-01-19 15:45:09
Storing analysis in StatusDB for frankhusky
Running command /home/proj/stage/bin/miniconda3/bin/conda run --name S_mutant /home/proj/stage/bin/miniconda3/envs/S_mutant/bin/mutant --version
Call ['/home/proj/stage/bin/miniconda3/bin/conda run --name S_mutant', '/home/proj/stage/bin/miniconda3/envs/S_mutant/bin/mutant', '--version'] exit with a non zero exit code
Traceback (most recent call last):
  File "/home/proj/stage/bin/miniconda3/envs/S_mutant/bin/mutant", line 10, in <module>
    from importlib.metadata import distribution
ModuleNotFoundError: No module named 'importlib.metadata'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/proj/stage/bin/miniconda3/envs/S_mutant/bin/mutant", line 13, in <module>
    from importlib_metadata import distribution
ModuleNotFoundError: No module named 'importlib_metadata'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/proj/stage/bin/miniconda3/envs/S_mutant/bin/mutant", line 15, in <module>
    from pkg_resources import load_entry_point
  File "/home/proj/stage/bin/miniconda3/envs/S_mutant/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3259, in <module>
    @_call_aside
  File "/home/proj/stage/bin/miniconda3/envs/S_mutant/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3234, in _call_aside
    f(*args, **kwargs)
  File "/home/proj/stage/bin/miniconda3/envs/S_mutant/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3272, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/home/proj/stage/bin/miniconda3/envs/S_mutant/lib/python3.7/site-packages/pkg_resources/__init__.py", line 581, in _build_master
    ws.require(__requires__)
  File "/home/proj/stage/bin/miniconda3/envs/S_mutant/lib/python3.7/site-packages/pkg_resources/__init__.py", line 909, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/home/proj/stage/bin/miniconda3/envs/S_mutant/lib/python3.7/site-packages/pkg_resources/__init__.py", line 795, in resolve
    raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'mutant' distribution was not found and is required by the application

ERROR conda.cli.main_run:execute(49): `conda run /home/proj/stage/bin/miniconda3/envs/S_mutant/bin/mutant --version` failed. (See above for error)
Could not retrieve mutant workflow version!
Analysis successfully stored in StatusDB: frankhusky : 2024-01-19 15:45:09
Action None set for case frankhusky

@henrikstranneheim henrikstranneheim marked this pull request as ready for review February 7, 2024 07:28
ivadym
ivadym approved these changes Feb 7, 2024
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Looks good 🧹 🧹

@henrikstranneheim henrikstranneheim merged commit 22ae40d into main Feb 8, 2024
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@henrikstranneheim henrikstranneheim deleted the refactor-pipeline-to-workflow branch February 8, 2024 07:32
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Deployed to production:

done.
Log deploy... done.
hermes version: 4.0.0

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