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Add validation step#22

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LouisLeNezet merged 68 commits intonf-core:devnf-core/phaseimpute:devfrom LouisLeNezet:validationLouisLeNezet/phaseimpute:validationCopy head branch name to clipboardApr 24, 2024

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Commits

Commits on Mar 26, 2024

• Add validation step

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  f58f958

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• Fix Eclint

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• Update table stats selection

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• Update changelog

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• Update changelog

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• Update changelog

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Commits on Mar 29, 2024

• Merge branch 'dev' into validation

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Commits on Apr 10, 2024

• Rename sbwf to glimpse1 and glimpse2

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• Separate simulation config

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Commits on Apr 11, 2024

• Separate configuration into each step and use full path

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• Update conf files

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• Add params for concordance analysis

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• VCF and BCF can now bbe use as input files

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• Update schema for validation params

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• Update modules

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• Fix schema

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• Update validation process to allow vcf and direct input

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Commits on Apr 12, 2024

• Update vcf_concordance_glimpse2 tests

  

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• Update config for all steps to spearate results files in corresponding folders

  

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• Add test for concordance analysis

  

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• Fix linting

  

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• Add check for extension (needs to be improved)

  

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Commits on Apr 16, 2024

• Merge branch 'dev' into validation

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• Add GL computation for bamg

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• Add multiqc

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Commits on Apr 17, 2024

• Update CHANGELOG.md

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• Remove glimpse concordance

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• Check works done

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• Remove panel index

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• Fix regions usage with null values for all genome analysis

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• Disable unecessary output results

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• Simplify channel

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• Test for only bam files for simulation process

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• Update tools

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• Fix changelog

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• Fix bam detection

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• Add coverage to multiqc

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• Remove version.yml export

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Commits on Apr 22, 2024

• Update conf/steps/imputation.config

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• Update conf/steps/panel_prep.config

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• Merge branch 'dev' into validation

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• Delete old module

  

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• Add gwak environment to add columns

  

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• Update running command

  

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• Delete trailing spaces

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• Add versions

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• Concatenate by chromosomes

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• Reorganize config

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• Rename concatenation script to main

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• Change version emission of addcolumns

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  b1ca5e5

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• Simplify concordance channel management

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• Add configurations

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• Concat by chromosomes

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• Add sbwf config files

  

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• Fix linting

  

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• Fix linting

  

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• Fix input channel

  

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• Compute bam list from tuple

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• Update quilt sbwf to compute bamlist from tuple

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• Join hap and legend by chromosomes

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• Rename output channel

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Commits on Apr 23, 2024

• Update quilt

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• Update quilt

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• Add annotation to genotype likelihood to set-id

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• Add annotation to quilt to set varians id

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• Remove merging of individuals for now and add it to road map

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Commits on Apr 24, 2024

• Update result directory configuration

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• Fix config

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