Code

add raredisease config#2725

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rannick merged 190 commits intomasterClinical-Genomics/cg:masterfrom add-raredisease-config-caseClinical-Genomics/cg:add-raredisease-config-caseCopy head branch name to clipboardMar 4, 2024

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Commits

Commits on Dec 1, 2023

• add raredisease config

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• typo

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• add samplesheet and pipeline parameters

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Commits on Dec 7, 2023

• update config case function

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• update config case function

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• update config case function

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• reach case_sample

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• reach case_sample

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• bug fixing

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• bug fixing

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• bug fixing

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• fix samplesheet creation

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• fix samplesheet creation

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• fix samplesheet creation

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Commits on Dec 11, 2023

• start plan for raredisease parameters

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Commits on Jan 9, 2024

• Merge branch 'master' into add-raredisease-config-case

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• fix linting

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Commits on Jan 11, 2024

• use general tower binary path

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• change to staticmethod and clean up sonarcloud issue

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• start preparing test for cg workflow raredisease config-case

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Commits on Jan 16, 2024

• comment out part of the test

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Commits on Jan 22, 2024

• move option_from_start to common

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• move option_from_start to common

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• move option_from_start to common

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• add config manipulation

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• merge

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• fix path

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• add on-the-fly parameters

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• add on-the-fly parameters, fix typo

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• add on-the-fly parameters, fix typo

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Commits on Jan 24, 2024

• fix PipelineParameters

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• config: write to stdout

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• config: write to stdout

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• add newline

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• add newline

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• fix some code smells

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• keep using RnafusionParameters

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• change type

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• update docstring

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• Merge branch 'master' into add-raredisease-config-case

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• uncomment tests

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• adapt server fixture

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• get parameters info in dry-run

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• remove binary path from raredisease server fixture

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• add outdir

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• add all pipeline parameter to teh string

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Commits on Feb 5, 2024

• Merge branch 'master' into add-raredisease-config-case

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• fix issues

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Commits on Feb 12, 2024

• Update cg/cli/workflow/nf_analysis.py

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• add config file extension and use

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• add config file extension and use

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• remove config read/write/concat that can be in txt io

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• Update cg/meta/workflow/raredisease.py

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• Update cg/meta/workflow/raredisease.py

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• Update cg/meta/workflow/raredisease.py

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• rename function config_case in RarediseaseApi

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• Merge branch 'add-raredisease-config-case' of https://github.com/Clinical-Genomics/cg into add-raredisease-config-case

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• Update cg/meta/workflow/raredisease.py

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• Update cg/meta/workflow/raredisease.py

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• use named arguments

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• Merge branch 'add-raredisease-config-case' of https://github.com/Clinical-Genomics/cg into add-raredisease-config-case

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• types and named args

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• use constant for empty string and double quote

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Commits on Feb 16, 2024

• use PlinkPhenotypeStatus + update docstring

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• use params instead of config, and overwrite nf-analysis in raredisease case, later to be moved in nf-analysis

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• clarify docstring

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• Update cg/models/raredisease/raredisease.py

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• use Sex class constants

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• move getting the parental id to StatusDB API

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• Merge branch 'add-raredisease-config-case' of https://github.com/Clinical-Genomics/cg into add-raredisease-config-case

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• move Pipeline to Workflow

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• create RarediseaseSampleSheetHeaders class, similar to Fluffy

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• add test raredisease config case

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• rename reformat function to clarify

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• Update cg/meta/workflow/raredisease.py

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• Update cg/meta/workflow/raredisease.py

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• update docstring

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• Merge branch 'add-raredisease-config-case' of https://github.com/Clinical-Genomics/cg into add-raredisease-config-case

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• samplesheet to sample sheet

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• fix dependencies

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• Merge branch 'master' into add-raredisease-config-case

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• fix dependencies

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• Merge branch 'add-raredisease-config-case' of https://github.com/Clinical-Genomics/cg into add-raredisease-config-case

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• workflow

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• workflow

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• fix dependencies

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• adapt concat

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Commits on Feb 29, 2024

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• Merge branch 'master' into add-raredisease-config-case

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• update dry-run message in tests

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• Merge branch 'add-raredisease-config-case' of https://github.com/Clinical-Genomics/cg into add-raredisease-config-case

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• Merge branch 'master' into add-raredisease-config-case

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• add test for concat

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• Merge branch 'add-raredisease-config-case' of https://github.com/Clinical-Genomics/cg into add-raredisease-config-case

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• continue addind concat tests

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• continue addind concat tests

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• fix typo

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• fix tests

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• fix tests

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• fix tests

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• Merge branch 'master' into add-raredisease-config-case

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• fix tests

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• Merge branch 'master' into add-raredisease-config-case

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• Merge branch 'add-raredisease-config-case' of https://github.com/Clinical-Genomics/cg into add-raredisease-config-case

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• add test for sample sheet creation

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• add test for sample sheet creation

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Commits on Mar 1, 2024

• test writing

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• test for writing config file

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• type for raredisease config to str

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• test for writing config file

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• test for writing config file

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Commits on Mar 4, 2024

• test for writing config file

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• make reformat_sample_content a property

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• Merge branch 'master' into add-raredisease-config-case

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• fix error

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• Merge branch 'add-raredisease-config-case' of https://github.com/Clinical-Genomics/cg into add-raredisease-config-case

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• Update cg/io/config.py

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• Update cg/meta/workflow/raredisease.py

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• Merge branch 'master' into add-raredisease-config-case

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• key to parameters

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• merge

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• Update cg/io/txt.py

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• Update cg/store/models.py

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• Merge branch 'add-raredisease-config-case' of https://github.com/Clinical-Genomics/cg into add-raredisease-config-case

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• parental id as property

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• parental id as property

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• parental id as property

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• parental id as property

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• paternal/maternal ids cannot be None, should return empty string

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